DEGs comparison in Day50 Cortical Brain Organoids
Oliviero Leonardi
January 13, 2025
library(UpSetR)
library(RNASeqBulkExploratory)
library(ggplot2)
library(DESeq2)
library(dplyr)
library(ggvenn)
## Loading required package: scales
##
## Attaching package: 'scales'
## The following object is masked from 'package:viridis':
##
## viridis_pal
library(gplots)
##
## Attaching package: 'gplots'
## The following object is masked from 'package:IRanges':
##
## space
## The following object is masked from 'package:S4Vectors':
##
## space
## The following object is masked from 'package:stats':
##
## lowess1. Environment Set Up
for (i in 1:length(params))
print(paste('Parameter:', names(params)[i], ' - Value:', params[[i]], '- Class:', class(params[[i]])))
## [1] "Parameter: Dataset - Value: CHD2_iPSCs_and_organoids_PublicRepo - Class: character"
## [1] "Parameter: InputFolder - Value: /group/testa/Project/CHD2/BulkRNAseq/results/PublicRepo/2.DEA/ - Class: character"
## [1] "Parameter: OutputFolder - Value: /group/testa/Project/CHD2/BulkRNAseq/results/PublicRepo/9.DEGsComparison/ - Class: character"
## [1] "Parameter: FDRthr - Value: 0.05 - Class: numeric"
## [1] "Parameter: logFCthr - Value: 1.5 - Class: numeric"logFCthr <- params$logFCthr
FDRthr <- params$FDRthrDEGs are thresholded for Overlap Analysis:
FDR threshold: 0.05
LogFC threshold: 1.5
2. Data Upload
DEA for iPSCs
DEAList_ips_HT <- readRDS(paste0(params$InputFolder, 'iPSCs/Output/Savings/ipsc.DEAList_HT.rds'))
DEAList_ips_AR <- readRDS(paste0(params$InputFolder, 'iPSCs/Output/Savings/ipsc.DEAList_AR.rds'))
DEAList_ips_HT
## $dds
## class: DESeqDataSet
## dim: 16981 9
## metadata(1): version
## assays(4): counts mu H cooks
## rownames(16981): TSPAN6 TNMD ... C8orf44 PDCD6-AHRR
## rowData names(39): Gene EnsGene ... deviance maxCooks
## colnames(9): OLE_001 OLE_002 ... OLE_029 OLE_030
## colData names(12): SampleNumber SampleID_GU ... lib.size sizeFactor
##
## $HT
## $HT$res
## log2 fold change (MLE): Genotype HT vs WT
## Wald test p-value: Genotype HT vs WT
## DataFrame with 16981 rows and 6 columns
## baseMean log2FoldChange lfcSE stat pvalue padj
## <numeric> <numeric> <numeric> <numeric> <numeric> <numeric>
## TSPAN6 1839.212 0.5049494 0.169534 2.978448 2.89712e-03 1.76964e-02
## TNMD 50.023 2.5175864 0.457319 5.505093 3.68973e-08 7.60379e-07
## DPM1 913.160 0.0795911 0.105715 0.752885 4.51519e-01 6.61882e-01
## SCYL3 150.087 -0.0606176 0.197933 -0.306253 7.59412e-01 8.78588e-01
## C1orf112 597.036 -0.1724953 0.200097 -0.862060 3.88655e-01 6.07051e-01
## ... ... ... ... ... ... ...
## FAM106C 3.59606 -2.331598 1.440608 -1.618482 1.05559e-01 2.66579e-01
## DUS4L-BCAP29 123.17497 -0.572171 0.274235 -2.086427 3.69399e-02 1.26569e-01
## ZCCHC14-DT 2.78524 -0.907292 1.352475 -0.670838 5.02323e-01 7.04955e-01
## C8orf44 59.84408 -0.182321 0.324451 -0.561938 5.74159e-01 7.59580e-01
## PDCD6-AHRR 14.92594 20.246746 3.778515 5.358387 8.39684e-08 1.61297e-06
##
## $HT$DEGs
## baseMean log2FoldChange lfcSE stat pvalue padj
## TNMD 50.023016 2.5175864 0.45731947 5.505093 3.689727e-08 7.603792e-07
## ENPP4 120.688084 -0.7240605 0.24421627 -2.964833 3.028472e-03 1.836004e-02
## SEMA3F 981.569865 0.6190299 0.20863088 2.967106 3.006174e-03 1.823789e-02
## CFTR 35.639635 -3.0173557 0.61695253 -4.890742 1.004565e-06 1.598737e-05
## CD99 1160.492056 0.5887600 0.16556063 3.556160 3.763156e-04 3.258652e-03
## HS3ST1 8.109638 2.7762536 0.85194713 3.258716 1.119177e-03 8.090567e-03
## AOC1 3.937746 -4.6357847 1.59275752 -2.910540 3.608046e-03 2.109788e-02
## KLHL13 256.664221 -0.8484196 0.21147493 -4.011916 6.022795e-05 6.452560e-04
## CFLAR 456.007078 0.5958769 0.14735164 4.043911 5.256689e-05 5.714714e-04
## TFPI 72.040033 0.8425149 0.30125966 2.796640 5.163697e-03 2.819445e-02
## MTMR7 237.606177 -0.7251733 0.18958920 -3.824972 1.307871e-04 1.278582e-03
## SARM1 150.728970 -0.9917129 0.22460403 -4.415384 1.008310e-05 1.294189e-04
## HSPB6 14.175341 2.4452045 0.61862535 3.952642 7.729304e-05 8.062120e-04
## TSPOAP1 218.325261 -0.8755312 0.19503823 -4.489024 7.155037e-06 9.484753e-05
## CROT 78.763633 -0.9719655 0.30672682 -3.168831 1.530532e-03 1.052059e-02
## SOX8 310.520774 1.3514849 0.20759357 6.510244 7.502868e-11 2.324931e-09
## CRLF1 523.506223 3.6889380 0.30274769 12.184859 3.742991e-34 9.347020e-32
## MAP3K14 155.019414 -1.1746157 0.24223979 -4.848979 1.240984e-06 1.928726e-05
## TAC1 18.033082 -1.8776176 0.60080309 -3.125180 1.776964e-03 1.187043e-02
## CX3CL1 39.008169 -3.1649608 0.53120505 -5.958077 2.552225e-09 6.317688e-08
## CACNA1G 149.062043 1.3239452 0.22418550 5.905579 3.514097e-09 8.524698e-08
## PROM1 2072.162377 0.7872385 0.15813341 4.978319 6.413893e-07 1.057421e-05
## NOS2 36.755957 -1.7773442 0.45356703 -3.918592 8.906769e-05 9.133203e-04
## DNAH9 15.995602 2.6872842 0.66435580 4.044947 5.233489e-05 5.693138e-04
## TRAPPC6A 371.386712 0.6959821 0.24133312 2.883906 3.927754e-03 2.260156e-02
## RHBDF1 618.713378 0.7729502 0.15308944 5.049010 4.441043e-07 7.511291e-06
## BAIAP3 202.677197 1.0649157 0.20483420 5.198915 2.004548e-07 3.617347e-06
## MYLIP 895.189470 1.0121983 0.13694071 7.391508 1.451730e-13 6.504440e-12
## SYN1 182.102239 -1.3278508 0.21052875 -6.307218 2.840952e-10 7.987121e-09
## JARID2 8224.824306 0.6261954 0.12760213 4.907406 9.228890e-07 1.478451e-05
## CAMK1G 14.681606 -1.6705286 0.63227040 -2.642111 8.239104e-03 4.061197e-02
## DLEC1 22.924327 -1.3220174 0.49967037 -2.645779 8.150304e-03 4.031469e-02
## CYB561 743.938862 0.8790001 0.14295685 6.148709 7.811611e-10 2.053390e-08
## AASS 13696.295658 -1.0911766 0.12640461 -8.632411 6.007203e-18 4.180669e-16
## NFIX 6.488386 4.4228073 1.40238636 3.153772 1.611748e-03 1.094326e-02
## ST3GAL1 181.289712 1.0278185 0.18300596 5.616312 1.950768e-08 4.182574e-07
## MMP25 1265.400734 1.5078652 0.12270101 12.288939 1.038604e-34 2.755707e-32
## REV3L 355.305028 -0.7006671 0.22764692 -3.077868 2.084875e-03 1.355927e-02
## TENM1 218.272449 2.0145807 0.21905667 9.196619 3.693906e-20 3.015684e-18
## PAX7 15.224684 3.0697407 0.67784484 4.528677 5.935401e-06 8.055929e-05
## CD9 2216.110308 1.2701616 0.11392235 11.149363 7.212064e-29 1.200667e-26
## SEMA3G 90.965836 -1.3530119 0.29194892 -4.634413 3.579514e-06 5.056883e-05
## STAB1 18.714620 -3.1847356 0.72317133 -4.403847 1.063481e-05 1.357818e-04
## IDS 836.079003 -0.9520371 0.17369914 -5.480954 4.230374e-08 8.596665e-07
## PRSS3 4.067363 -5.1203416 1.55386502 -3.295229 9.834139e-04 7.279577e-03
## CD4 102.129267 -0.8295457 0.30406343 -2.728199 6.368111e-03 3.308962e-02
## FYN 1036.538766 -0.7137789 0.17228511 -4.143010 3.427770e-05 3.903338e-04
## MRC2 883.198304 0.9174997 0.13363935 6.865491 6.626316e-12 2.383930e-10
## TSPAN9 908.111816 0.6230343 0.15371935 4.053064 5.055126e-05 5.506164e-04
## PLAUR 169.478993 1.1892446 0.20893456 5.691948 1.255982e-08 2.809992e-07
## MAN2B2 237.658159 0.8106847 0.22195737 3.652434 2.597663e-04 2.354794e-03
## SLC7A14 14.537574 -2.0787110 0.72604902 -2.863045 4.195910e-03 2.386160e-02
## CLDN11 85.160769 1.2571120 0.29574130 4.250715 2.130892e-05 2.528628e-04
## DPEP1 408.259255 -3.3589338 0.26362093 -12.741529 3.475144e-37 1.092804e-34
## IL20RA 45.434941 -0.9372377 0.31773033 -2.949790 3.179903e-03 1.910079e-02
## ATP1A2 1254.559680 -1.9984784 0.20292121 -9.848543 6.954444e-23 7.380838e-21
## ZNF582 91.316247 -1.1544838 0.27761270 -4.158613 3.201856e-05 3.683653e-04
## SYT13 371.170624 -0.8854705 0.18597067 -4.761345 1.923068e-06 2.874614e-05
## CD74 514.416139 -1.2949383 0.23089421 -5.608362 2.042505e-08 4.362739e-07
## ADGRA2 172.234754 2.9760245 0.20737916 14.350644 1.055530e-46 7.468314e-44
## RUNX3 13.116324 1.8545069 0.72026182 2.574768 1.003074e-02 4.719646e-02
## PLEKHB1 254.938718 -2.1675004 0.25734320 -8.422606 3.682008e-17 2.368340e-15
## OSBPL5 246.312599 0.9031717 0.28000578 3.225547 1.257323e-03 8.892377e-03
## CPS1 559.102986 -2.0546093 0.18018758 -11.402614 4.057518e-30 7.177158e-28
## FHL1 708.258743 -0.8951035 0.16578221 -5.399273 6.691133e-08 1.310520e-06
## GRAMD1B 533.862445 -0.8441858 0.27052746 -3.120518 1.805333e-03 1.201324e-02
## DEF6 175.979327 0.7777296 0.27820873 2.795489 5.182119e-03 2.826777e-02
## EHD2 303.678788 -1.2919955 0.22067584 -5.854721 4.778116e-09 1.136375e-07
## RRAGD 415.127177 0.6233723 0.22668537 2.749945 5.960525e-03 3.149212e-02
## VIM 940.982385 -1.6294965 0.19164618 -8.502630 1.853437e-17 1.205870e-15
## FAS 56.880016 -2.6852826 0.47405773 -5.664463 1.474855e-08 3.231550e-07
## RNASET2 401.405612 0.6548899 0.20692002 3.164942 1.551138e-03 1.061663e-02
## CD44 78.713158 -1.1735390 0.27941405 -4.200000 2.669149e-05 3.110832e-04
## KCNG1 460.398241 0.9124319 0.21140631 4.316011 1.588741e-05 1.940893e-04
## BTN3A1 105.847835 -0.9792877 0.34994795 -2.798381 5.135947e-03 2.809714e-02
## PRKCH 215.006991 1.3909029 0.30052789 4.628199 3.688592e-06 5.180809e-05
## HMGB3 8214.937656 0.8097357 0.12578924 6.437241 1.216644e-10 3.637295e-09
## ARHGAP31 224.278647 2.2802469 0.26549779 8.588572 8.805698e-18 5.957353e-16
## APBA2 504.735180 0.6669969 0.13912039 4.794386 1.631735e-06 2.485067e-05
## TMSB10 7559.539981 1.0077127 0.15262170 6.602683 4.037818e-11 1.308515e-09
## DAPK2 34.573991 -1.3991118 0.47744349 -2.930424 3.385000e-03 2.006307e-02
## TIMP2 1179.047488 0.8555700 0.12695661 6.739074 1.593987e-11 5.512727e-10
## FLT4 311.776760 0.9237841 0.16356828 5.647698 1.626109e-08 3.540124e-07
## CDH1 7945.148949 0.6162606 0.14451441 4.264354 2.004816e-05 2.395133e-04
## DNAH5 16.705341 -1.8809808 0.59406870 -3.166268 1.544084e-03 1.059055e-02
## BEST2 41.914040 -1.5060966 0.43539420 -3.459156 5.418703e-04 4.428056e-03
## TNC 112.108829 -1.5243894 0.29838959 -5.108722 3.243453e-07 5.625850e-06
## CAPG 996.645533 0.9123606 0.24102520 3.785333 1.535030e-04 1.480201e-03
## GPM6B 1903.253264 0.6389611 0.13186365 4.845620 1.262171e-06 1.957345e-05
## ATP6V1H 753.543534 0.8202377 0.11230985 7.303347 2.806971e-13 1.215948e-11
## ARAP2 80.240829 -1.7003170 0.36602715 -4.645330 3.395328e-06 4.820742e-05
## FAM184B 11.472343 -2.6472198 0.79208111 -3.342107 8.314501e-04 6.374200e-03
## LMO3 514.967724 2.1902717 0.18955301 11.554930 6.970465e-31 1.345062e-28
## COL9A2 121.556929 1.5708096 0.31712809 4.953234 7.299021e-07 1.189488e-05
## PER3 306.465233 -0.9975477 0.20848832 -4.784669 1.712690e-06 2.588002e-05
## EPN3 128.113525 1.9294358 0.22399709 8.613665 7.076154e-18 4.845168e-16
## LTBP1 1496.357212 0.7230251 0.13491544 5.359098 8.363839e-08 1.608452e-06
## PPP1R3F 171.272506 -0.6425219 0.21362207 -3.007750 2.631891e-03 1.641886e-02
## NEXMIF 29.754512 -1.4492828 0.52030062 -2.785472 5.344987e-03 2.894235e-02
## LAMC3 1465.199421 1.6712541 0.20942703 7.980126 1.461838e-15 8.007570e-14
## COL23A1 491.493590 1.0759317 0.25902141 4.153833 3.269518e-05 3.741219e-04
## HERPUD1 427.813849 0.6633018 0.16113945 4.116322 3.849671e-05 4.320639e-04
## HOMER3 469.067082 0.7202037 0.23718701 3.036438 2.393913e-03 1.514569e-02
## PRSS8 2016.894882 0.6840759 0.19474061 3.512754 4.434874e-04 3.750428e-03
## FSTL4 80.135907 -0.7450135 0.28725481 -2.593563 9.498704e-03 4.530323e-02
## NNAT 765.967350 2.2007744 0.14728942 14.941836 1.760565e-50 1.660898e-47
## ENTPD2 81.875793 0.9002594 0.29444422 3.057487 2.232013e-03 1.431534e-02
## LY75 65.271233 -1.4927578 0.43928733 -3.398135 6.784686e-04 5.351173e-03
## SDCCAG8 153.028843 0.9812737 0.24752960 3.964268 7.362152e-05 7.711969e-04
## FOXC1 162.492186 7.7712273 1.12352274 6.916840 4.618282e-12 1.693802e-10
## SYNE2 3649.954266 0.9123672 0.15151617 6.021583 1.727194e-09 4.332273e-08
## ATP9A 557.565064 -0.8385044 0.24114155 -3.477229 5.066251e-04 4.180273e-03
## KCNH2 330.101458 1.0610931 0.30149366 3.519454 4.324362e-04 3.678957e-03
## EIF2AK2 2561.318175 -0.8191185 0.15898472 -5.152183 2.574710e-07 4.535388e-06
## NPFFR2 58.683708 1.9178066 0.38161934 5.025444 5.022691e-07 8.436233e-06
## TRAF3IP2 483.881342 1.0727380 0.15980331 6.712864 1.908405e-11 6.533594e-10
## SERPINB3 30.828152 -8.2133249 1.34765345 -6.094538 1.097541e-09 2.819567e-08
## F7 13.880892 -2.1693636 0.80534589 -2.693704 7.066285e-03 3.599058e-02
## CDK14 1098.121727 1.1000754 0.13823453 7.958036 1.747912e-15 9.513237e-14
## PTPRU 1508.517016 0.6902236 0.16314326 4.230782 2.328798e-05 2.740554e-04
## RIMBP2 31.504709 2.2750683 0.40056856 5.679598 1.350118e-08 2.995360e-07
## GUCY1B1 118.008038 2.6523076 0.34604769 7.664573 1.794277e-14 8.831485e-13
## TNK2 1065.177832 0.6025731 0.19017914 3.168450 1.532540e-03 1.052059e-02
## DGAT2 61.567664 -1.4337723 0.39095898 -3.667322 2.451045e-04 2.237698e-03
## SEZ6 62.433943 -2.6235166 0.44921196 -5.840264 5.211806e-09 1.236057e-07
## CA11 1157.331236 -0.9119232 0.24159745 -3.774556 1.602927e-04 1.538969e-03
## TM7SF3 1459.830219 -0.7387118 0.09760295 -7.568540 3.774432e-14 1.795340e-12
## DLX3 9.322955 2.8108034 0.83252168 3.376252 7.348045e-04 5.734244e-03
## ATP2C2 55.201458 1.0992590 0.38481431 2.856596 4.282104e-03 2.426240e-02
## NGFR 156.818745 1.1198266 0.23733247 4.718387 2.377214e-06 3.476957e-05
## SLC12A2 378.045680 -0.6870590 0.24745010 -2.776556 5.493822e-03 2.955584e-02
## CALCRL 47.728614 -1.5349437 0.37008883 -4.147501 3.361245e-05 3.835841e-04
## OAT 2009.440607 1.3344562 0.13805208 9.666324 4.191647e-22 4.162477e-20
## NTN1 96.163904 0.9315215 0.32288935 2.884956 3.914685e-03 2.254163e-02
## SNAP91 22.910533 -1.5123603 0.55544964 -2.722768 6.473756e-03 3.353595e-02
## COL17A1 39.792053 -1.4127033 0.40004673 -3.531346 4.134512e-04 3.531597e-03
## TLE2 200.372276 2.2458430 0.33048238 6.795651 1.078244e-11 3.822475e-10
## FAM107B 662.747739 0.8711286 0.13624045 6.394052 1.615461e-10 4.721540e-09
## ME1 227.388590 -0.7693135 0.16806421 -4.577498 4.705712e-06 6.512444e-05
## CTNNA2 132.018902 -0.9224598 0.23081534 -3.996527 6.427847e-05 6.817694e-04
## TIE1 58.637160 -1.2862725 0.40335398 -3.188942 1.427944e-03 9.929533e-03
## MPPED2 44.686786 -1.0783944 0.33613577 -3.208211 1.335636e-03 9.360478e-03
## FECH 620.166821 -0.7193559 0.14995302 -4.797209 1.608918e-06 2.452517e-05
## PFKP 2332.396435 -0.6026955 0.13009963 -4.632568 3.611569e-06 5.093692e-05
## PHKA1 373.951019 0.6072118 0.17885549 3.394985 6.863229e-04 5.398077e-03
## PDK3 1386.343233 0.6890946 0.10612045 6.493513 8.385737e-11 2.573030e-09
## PYGM 134.330454 -0.6875300 0.24184695 -2.842831 4.471475e-03 2.505945e-02
## SDK2 731.209823 1.5152087 0.28630525 5.292284 1.207981e-07 2.266600e-06
## BCL3 47.387774 1.7422493 0.42178052 4.130701 3.616582e-05 4.088760e-04
## MAOB 48.593603 -1.0612869 0.31928356 -3.323964 8.874777e-04 6.694918e-03
## PIGB 104.420622 -0.6796502 0.22587102 -3.009019 2.620928e-03 1.636851e-02
## RAB27A 169.597782 -0.6133747 0.21809805 -2.812381 4.917627e-03 2.705093e-02
## NUCB2 345.511309 -0.8853450 0.15884301 -5.573711 2.493694e-08 5.293177e-07
## WIPI1 295.583513 1.1593150 0.23906766 4.849317 1.238871e-06 1.928255e-05
## ASNS 4133.305247 1.0099430 0.36793335 2.744907 6.052797e-03 3.184844e-02
## PTPN21 531.666906 -0.9236141 0.16752265 -5.513368 3.520304e-08 7.316803e-07
## OSBPL3 475.275198 0.8563552 0.17561902 4.876210 1.081435e-06 1.708264e-05
## NCK2 1705.958584 0.5850421 0.14355708 4.075328 4.594958e-05 5.079882e-04
## RPS6KA2 783.616890 0.9986531 0.15465240 6.457404 1.065142e-10 3.218360e-09
## TRIB2 1516.829531 0.9360330 0.14024578 6.674233 2.485283e-11 8.394336e-10
## LIMS2 45.633961 -1.6630993 0.41605130 -3.997342 6.405772e-05 6.801176e-04
## SREBF1 2410.892025 0.6313895 0.15737315 4.012054 6.019277e-05 6.452560e-04
## TRNT1 416.582301 -0.8270990 0.17294398 -4.782468 1.731561e-06 2.611335e-05
## ACAP1 328.109251 -1.0651817 0.21833566 -4.878643 1.068182e-06 1.688902e-05
## CRMP1 2921.222256 1.3845083 0.11824580 11.708732 1.149869e-31 2.352520e-29
## ADAM11 130.541352 -0.5928451 0.20330697 -2.916010 3.545392e-03 2.081753e-02
## [ reached 'max' / getOption("max.print") -- omitted 2408 rows ]
##
## $HT$resAshr
## log2 fold change (MMSE): Genotype HT vs WT
## Wald test p-value: Genotype HT vs WT
## DataFrame with 16981 rows and 5 columns
## baseMean log2FoldChange lfcSE pvalue padj
## <numeric> <numeric> <numeric> <numeric> <numeric>
## TSPAN6 1839.212 0.3601871 0.1780761 2.89712e-03 1.76964e-02
## TNMD 50.023 2.2521088 0.4685196 3.68973e-08 7.60379e-07
## DPM1 913.160 0.0598697 0.0919778 4.51519e-01 6.61882e-01
## SCYL3 150.087 -0.0301068 0.1398662 7.59412e-01 8.78588e-01
## C1orf112 597.036 -0.0865917 0.1450572 3.88655e-01 6.07051e-01
## ... ... ... ... ... ...
## FAM106C 3.59606 -0.299826 0.690995 1.05559e-01 2.66579e-01
## DUS4L-BCAP29 123.17497 -0.287169 0.252811 3.69399e-02 1.26569e-01
## ZCCHC14-DT 2.78524 -0.091265 0.454908 5.02323e-01 7.04955e-01
## C8orf44 59.84408 -0.059125 0.189225 5.74159e-01 7.59580e-01
## PDCD6-AHRR 14.92594 12.530118 3.449307 8.39684e-08 1.61297e-06
##
## $HT$DEGsAshr
## baseMean log2FoldChange lfcSE pvalue padj
## TNMD 50.023016 2.2521088 0.4685196 3.689727e-08 7.603792e-07
## CFTR 35.639635 -2.5732161 0.6584404 1.004565e-06 1.598737e-05
## HS3ST1 8.109638 1.6071214 1.0290554 1.119177e-03 8.090567e-03
## AOC1 3.937746 -1.3855103 1.6906527 3.608046e-03 2.109788e-02
## KLHL13 256.664221 -0.7432323 0.2449716 6.022795e-05 6.452560e-04
## MTMR7 237.606177 -0.6113749 0.2234354 1.307871e-04 1.278582e-03
## SARM1 150.728970 -0.9053621 0.2443980 1.008310e-05 1.294189e-04
## HSPB6 14.175341 1.9061709 0.6849187 7.729304e-05 8.062120e-04
## TSPOAP1 218.325261 -0.8015765 0.2158768 7.155037e-06 9.484753e-05
## CROT 78.763633 -0.7206616 0.3731804 1.530532e-03 1.052059e-02
## SOX8 310.520774 1.2927871 0.2070244 7.502868e-11 2.324931e-09
## CRLF1 523.506223 3.6182315 0.3087240 3.742991e-34 9.347020e-32
## MAP3K14 155.019414 -1.0905843 0.2490714 1.240984e-06 1.928726e-05
## TAC1 18.033082 -1.1978268 0.7166493 1.776964e-03 1.187043e-02
## CX3CL1 39.008169 -2.8603633 0.5601812 2.552225e-09 6.317688e-08
## CACNA1G 149.062043 1.2555713 0.2239040 3.514097e-09 8.524698e-08
## PROM1 2072.162377 0.7356813 0.1727412 6.413893e-07 1.057421e-05
## NOS2 36.755957 -1.4644857 0.4938284 8.906769e-05 9.133203e-04
## DNAH9 15.995602 2.0940670 0.7382690 5.233489e-05 5.693138e-04
## RHBDF1 618.713378 0.7235989 0.1671261 4.441043e-07 7.511291e-06
## BAIAP3 202.677197 1.0053635 0.2099293 2.004548e-07 3.617347e-06
## MYLIP 895.189470 0.9877661 0.1370771 1.451730e-13 6.504440e-12
## SYN1 182.102239 -1.2676126 0.2099951 2.840952e-10 7.987121e-09
## CAMK1G 14.681606 -0.8220175 0.7032247 8.239104e-03 4.061197e-02
## DLEC1 22.924327 -0.7223058 0.5719810 8.150304e-03 4.031469e-02
## CYB561 743.938862 0.8491047 0.1467250 7.811611e-10 2.053390e-08
## AASS 13696.295658 -1.0702605 0.1261122 6.007203e-18 4.180669e-16
## NFIX 6.488386 1.8136722 1.7173830 1.611748e-03 1.094326e-02
## ST3GAL1 181.289712 0.9814334 0.1860950 1.950768e-08 4.182574e-07
## MMP25 1265.400734 1.4869531 0.1226916 1.038604e-34 2.755707e-32
## TENM1 218.272449 1.9500646 0.2198154 3.693906e-20 3.015684e-18
## PAX7 15.224684 2.5261506 0.7396790 5.935401e-06 8.055929e-05
## CD9 2216.110308 1.2524610 0.1137531 7.212064e-29 1.200667e-26
## SEMA3G 90.965836 -1.2312132 0.2998878 3.579514e-06 5.056883e-05
## STAB1 18.714620 -2.5725913 0.8045609 1.063481e-05 1.357818e-04
## IDS 836.079003 -0.9079732 0.1791343 4.230374e-08 8.596665e-07
## PRSS3 4.067363 -2.2295021 2.0253663 9.834139e-04 7.279577e-03
## FYN 1036.538766 -0.6242334 0.1997312 3.427770e-05 3.903338e-04
## MRC2 883.198304 0.8933721 0.1351033 6.626316e-12 2.383930e-10
## PLAUR 169.478993 1.1300722 0.2096937 1.255982e-08 2.809992e-07
## MAN2B2 237.658159 0.6721013 0.2647263 2.597663e-04 2.354794e-03
## SLC7A14 14.537574 -1.0732431 0.8342941 4.195910e-03 2.386160e-02
## CLDN11 85.160769 1.1220588 0.3153850 2.130892e-05 2.528628e-04
## DPEP1 408.259255 -3.2954297 0.2679488 3.475144e-37 1.092804e-34
## IL20RA 45.434941 -0.6429320 0.3828441 3.179903e-03 1.910079e-02
## ATP1A2 1254.559680 -1.9430461 0.2035211 6.954444e-23 7.380838e-21
## ZNF582 91.316247 -1.0279645 0.3023202 3.201856e-05 3.683653e-04
## SYT13 371.170624 -0.8237021 0.2013247 1.923068e-06 2.874614e-05
## CD74 514.416139 -1.2222721 0.2312085 2.042505e-08 4.362739e-07
## ADGRA2 172.234754 2.9295759 0.2092814 1.055530e-46 7.468314e-44
## RUNX3 13.116324 0.8132997 0.7664458 1.003074e-02 4.719646e-02
## PLEKHB1 254.938718 -2.0799439 0.2588130 3.682008e-17 2.368340e-15
## OSBPL5 246.312599 0.6822974 0.3400291 1.257323e-03 8.892377e-03
## CPS1 559.102986 -2.0112063 0.1806459 4.057518e-30 7.177158e-28
## FHL1 708.258743 -0.8521347 0.1732540 6.691133e-08 1.310520e-06
## GRAMD1B 533.862445 -0.6173684 0.3266069 1.805333e-03 1.201324e-02
## EHD2 303.678788 -1.2258576 0.2205391 4.778116e-09 1.136375e-07
## VIM 940.982385 -1.5787570 0.1917393 1.853437e-17 1.205870e-15
## FAS 56.880016 -2.4091201 0.4888209 1.474855e-08 3.231550e-07
## CD44 78.713158 -1.0478735 0.3021954 2.669149e-05 3.110832e-04
## KCNG1 460.398241 0.8261015 0.2356891 1.588741e-05 1.940893e-04
## BTN3A1 105.847835 -0.6259525 0.4154034 5.135947e-03 2.809714e-02
## PRKCH 215.006991 1.2622131 0.3082738 3.688592e-06 5.180809e-05
## HMGB3 8214.937656 0.7846510 0.1299879 1.216644e-10 3.637295e-09
## ARHGAP31 224.278647 2.1884948 0.2673574 8.805698e-18 5.957353e-16
## APBA2 504.735180 0.6083904 0.1561810 1.631735e-06 2.485067e-05
## TMSB10 7559.539981 0.9768376 0.1533985 4.037818e-11 1.308515e-09
## DAPK2 34.573991 -0.8895045 0.5722080 3.385000e-03 2.006307e-02
## TIMP2 1179.047488 0.8323932 0.1295492 1.593987e-11 5.512727e-10
## FLT4 311.776760 0.8845133 0.1686246 1.626109e-08 3.540124e-07
## DNAH5 16.705341 -1.2241736 0.7086132 1.544084e-03 1.059055e-02
## BEST2 41.914040 -1.1605079 0.5090819 5.418703e-04 4.428056e-03
## TNC 112.108829 -1.4014187 0.3000735 3.243453e-07 5.625850e-06
## CAPG 996.645533 0.7784483 0.2828417 1.535030e-04 1.480201e-03
## ATP6V1H 753.543534 0.8018084 0.1144714 2.806971e-13 1.215948e-11
## ARAP2 80.240829 -1.5132036 0.3731216 3.395328e-06 4.820742e-05
## FAM184B 11.472343 -1.6414593 0.9534324 8.314501e-04 6.374200e-03
## LMO3 514.967724 2.1430498 0.1901748 6.970465e-31 1.345062e-28
## COL9A2 121.556929 1.4314405 0.3199455 7.299021e-07 1.189488e-05
## PER3 306.465233 -0.9295161 0.2203057 1.712690e-06 2.588002e-05
## EPN3 128.113525 1.8613948 0.2246919 7.076154e-18 4.845168e-16
## LTBP1 1496.357212 0.6812595 0.1466951 8.363839e-08 1.608452e-06
## NEXMIF 29.754512 -0.8384240 0.6100941 5.344987e-03 2.894235e-02
## LAMC3 1465.199421 1.6107888 0.2096012 1.461838e-15 8.007570e-14
## COL23A1 491.493590 0.9604675 0.2852627 3.269518e-05 3.741219e-04
## NNAT 765.967350 2.1723463 0.1475860 1.760565e-50 1.660898e-47
## ENTPD2 81.875793 0.6442738 0.3563482 2.232013e-03 1.431534e-02
## LY75 65.271233 -1.1319991 0.5177355 6.784686e-04 5.351173e-03
## SDCCAG8 153.028843 0.8593494 0.2825371 7.362152e-05 7.711969e-04
## FOXC1 162.492186 7.2748157 1.1348759 4.618282e-12 1.693802e-10
## SYNE2 3649.954266 0.8795419 0.1550761 1.727194e-09 4.332273e-08
## ATP9A 557.565064 -0.6734277 0.2902653 5.066251e-04 4.180273e-03
## KCNH2 330.101458 0.8627737 0.3583607 4.324362e-04 3.678957e-03
## EIF2AK2 2561.318175 -0.7723027 0.1708352 2.574710e-07 4.535388e-06
## NPFFR2 58.683708 1.7193603 0.3856310 5.022691e-07 8.436233e-06
## TRAF3IP2 483.881342 1.0390289 0.1599288 1.908405e-11 6.533594e-10
## SERPINB3 30.828152 -7.4918317 1.3667030 1.097541e-09 2.819567e-08
## F7 13.880892 -0.9511046 0.8714615 7.066285e-03 3.599058e-02
## CDK14 1098.121727 1.0749909 0.1379182 1.747912e-15 9.513237e-14
## PTPRU 1508.517016 0.6065077 0.1881633 2.328798e-05 2.740554e-04
## RIMBP2 31.504709 2.0644763 0.4062017 1.350118e-08 2.995360e-07
## GUCY1B1 118.008038 2.5064949 0.3521884 1.794277e-14 8.831485e-13
## DGAT2 61.567664 -1.1696497 0.4448005 2.451045e-04 2.237698e-03
## SEZ6 62.433943 -2.3730113 0.4611791 5.211806e-09 1.236057e-07
## CA11 1157.331236 -0.7767772 0.2838137 1.602927e-04 1.538969e-03
## TM7SF3 1459.830219 -0.7222063 0.1004903 3.774432e-14 1.795340e-12
## DLX3 9.322955 1.7308352 1.0090067 7.348045e-04 5.734244e-03
## ATP2C2 55.201458 0.7104228 0.4613474 4.282104e-03 2.426240e-02
## NGFR 156.818745 1.0364491 0.2472759 2.377214e-06 3.476957e-05
## CALCRL 47.728614 -1.3300169 0.3927711 3.361245e-05 3.835841e-04
## OAT 2009.440607 1.3083110 0.1378280 4.191647e-22 4.162477e-20
## NTN1 96.163904 0.6223985 0.3865091 3.914685e-03 2.254163e-02
## SNAP91 22.910533 -0.8263346 0.6401815 6.473756e-03 3.353595e-02
## COL17A1 39.792053 -1.1210586 0.4646038 4.134512e-04 3.531597e-03
## TLE2 200.372276 2.1024677 0.3337216 1.078244e-11 3.822475e-10
## FAM107B 662.747739 0.8442795 0.1393908 1.615461e-10 4.721540e-09
## ME1 227.388590 -0.7026279 0.1887658 4.705712e-06 6.512444e-05
## CTNNA2 132.018902 -0.8099654 0.2649293 6.427847e-05 6.817694e-04
## TIE1 58.637160 -0.9342005 0.4870382 1.427944e-03 9.929533e-03
## MPPED2 44.686786 -0.8053188 0.4082660 1.335636e-03 9.360478e-03
## FECH 620.166821 -0.6614984 0.1675619 1.608918e-06 2.452517e-05
## PDK3 1386.343233 0.6639277 0.1121757 8.385737e-11 2.573030e-09
## SDK2 731.209823 1.4023777 0.2871150 1.207981e-07 2.266600e-06
## BCL3 47.387774 1.4812960 0.4470573 3.616582e-05 4.088760e-04
## MAOB 48.593603 -0.8218037 0.3858224 8.874777e-04 6.694918e-03
## NUCB2 345.511309 -0.8463582 0.1652897 2.493694e-08 5.293177e-07
## WIPI1 295.583513 1.0771951 0.2461660 1.238871e-06 1.928255e-05
## ASNS 4133.305247 0.6259185 0.4334900 6.052797e-03 3.184844e-02
## PTPN21 531.666906 -0.8817621 0.1734212 3.520304e-08 7.316803e-07
## OSBPL3 475.275198 0.8000578 0.1899663 1.081435e-06 1.708264e-05
## RPS6KA2 783.616890 0.9667465 0.1557352 1.065142e-10 3.218360e-09
## TRIB2 1516.829531 0.9094918 0.1417579 2.485283e-11 8.394336e-10
## LIMS2 45.633961 -1.4007193 0.4484357 6.405772e-05 6.801176e-04
## TRNT1 416.582301 -0.7681388 0.1894316 1.731561e-06 2.611335e-05
## ACAP1 328.109251 -0.9947591 0.2269858 1.068182e-06 1.688902e-05
## CRMP1 2921.222256 1.3651798 0.1181540 1.149869e-31 2.352520e-29
## MAP3K13 86.469668 -5.8181731 0.7169905 1.748234e-17 1.146207e-15
## FRY 232.964767 -0.9316545 0.2464346 8.304650e-06 1.084779e-04
## PPP2R2C 266.194600 0.8818560 0.1983447 5.971592e-07 9.931793e-06
## ATP2A3 621.823576 0.9641604 0.2064955 3.071384e-07 5.343768e-06
## MGLL 25.276589 1.3829390 0.5570557 2.862851e-04 2.562681e-03
## LMAN1 2830.324995 -0.7947970 0.1000126 2.442038e-16 1.444887e-14
## KCNQ2 916.675310 1.0037192 0.1958389 4.237329e-08 8.596665e-07
## SEMA3C 53.015364 1.9813179 0.4246295 1.228791e-07 2.303101e-06
## GRAMD4 597.976839 0.8667563 0.2080881 1.714588e-06 2.588038e-05
## WNT8B 7.904379 -0.8873774 0.9075553 9.316804e-03 4.462868e-02
## FGF4 26.729090 3.3405509 0.5940399 8.394433e-11 2.573030e-09
## VPS9D1 104.798549 0.6682933 0.3601042 1.924849e-03 1.266894e-02
## ZNF37A 96.568800 4.5962140 1.1429425 3.051023e-07 5.319243e-06
## CACNG4 96.026048 0.8182299 0.4080936 1.224481e-03 8.707250e-03
## FSCN1 8776.866763 1.3715161 0.1393231 1.169512e-23 1.298005e-21
## TRAF4 3239.456673 0.5994841 0.1514121 1.209375e-06 1.884601e-05
## MCAM 469.858295 0.6366113 0.2658753 3.993115e-04 3.428063e-03
## IL4R 824.302440 0.7814571 0.2186518 1.091034e-05 1.384667e-04
## CAPN6 164.928131 -1.8751738 0.2340373 6.514863e-17 4.127944e-15
## NAALAD2 135.711789 1.0840915 0.2181812 9.863393e-08 1.871400e-06
## FBLN1 3061.849265 1.1498920 0.1276414 5.354839e-20 4.269039e-18
## NEBL 554.440907 -1.7165868 0.2408979 7.984745e-14 3.684483e-12
## ADCYAP1R1 363.989423 -0.8566939 0.1791412 1.271222e-07 2.369552e-06
## ITM2A 367.678214 1.0652218 0.1758327 2.944624e-10 8.264901e-09
## RUNX1T1 612.563495 0.7176010 0.1474016 3.694338e-08 7.604068e-07
## SLC1A3 759.140840 1.7123797 0.2049705 5.167360e-18 3.610985e-16
## FDFT1 10031.670273 0.6756250 0.1084655 1.415770e-11 4.916399e-10
## RIMS1 23.639614 -1.1750029 0.6621264 1.510776e-03 1.041538e-02
## MOXD1 92.085937 -1.2896019 0.2856183 7.113602e-07 1.162706e-05
## EPHA6 22.587819 -1.3951057 0.6152575 4.399298e-04 3.731492e-03
## SMARCA2 252.357350 1.0951221 0.2881547 9.829702e-06 1.263574e-04
## COL5A3 40.088982 -0.8621464 0.4906283 2.194378e-03 1.413609e-02
## CHRNA3 74.627518 2.3268584 0.3323636 6.030563e-14 2.813324e-12
## AFP 15.059954 -0.8129344 0.6881552 8.198269e-03 4.047875e-02
## MEF2C 18.573701 1.0326362 0.6508619 2.632862e-03 1.641888e-02
## CDC14B 2208.141077 1.1481881 0.1300931 2.787200e-19 2.057802e-17
## LRP2 58.041498 -0.8880912 0.4977485 2.016842e-03 1.316724e-02
## AACS 1206.364698 1.3215611 0.1025454 9.579459e-39 3.536278e-36
## PCDHA6 85.700980 5.0434833 0.4824361 4.504472e-27 6.769065e-25
## ATP8B1 174.449562 1.5698899 0.1897492 1.354941e-17 8.987598e-16
## IL12RB2 44.227342 -3.0114888 0.6295984 1.080735e-08 2.450196e-07
## SMARCD3 92.988690 1.2204619 0.2532877 1.981666e-07 3.579858e-06
## SERTAD4 97.634658 1.5922135 0.2560925 4.924238e-11 1.574736e-09
## GRHL2 966.401906 0.6661774 0.1346183 1.725766e-08 3.733150e-07
## P2RX5 77.942447 -1.3249567 0.3583354 1.349016e-05 1.678296e-04
## MECOM 95.586553 5.4399266 0.4693840 2.031519e-32 4.480160e-30
## TTC39A 110.918760 -1.2037853 0.3051202 6.289077e-06 8.455646e-05
## NME8 8.905710 1.0566152 0.9726193 5.630885e-03 3.006857e-02
## EPDR1 196.187785 -1.3352088 0.1985118 2.925507e-12 1.116360e-10
## SEPHS1 16750.668277 0.6852332 0.1627869 6.011328e-07 9.985157e-06
## FAT2 27.514823 -1.2665840 0.6910246 1.197981e-03 8.553816e-03
## MYBPC2 106.559788 -1.4011539 0.2631847 1.322179e-08 2.942584e-07
## TMPRSS11E 36.946326 2.1960725 0.4308838 9.640259e-09 2.209194e-07
## MMP2 1229.479440 1.4157988 0.1410738 1.544642e-24 1.847153e-22
## TFAP2C 279.948004 2.3208808 0.2641476 3.910778e-20 3.177461e-18
## DOCK3 361.908463 -0.9061087 0.2239924 3.061864e-06 4.398775e-05
## SMOX 184.941602 0.5936619 0.2321203 2.355212e-04 2.160662e-03
## F11 21.600248 1.7798861 0.5085462 1.473781e-05 1.814813e-04
## CHGB 55.167346 -1.3626201 0.3993194 3.056330e-05 3.540215e-04
## TBX5 124.839204 7.7869098 0.6924131 1.019221e-30 1.944651e-28
## GRAMD1A 4155.693890 1.4263305 0.1258104 1.223617e-30 2.283323e-28
## ANKRD24 262.545013 -1.3381464 0.2149976 7.862820e-11 2.423204e-09
## PCBP4 623.901957 1.2180983 0.1908087 3.492537e-11 1.144918e-09
## YPEL3 430.038339 0.6372106 0.1870250 1.248496e-05 1.568099e-04
## [ reached 'max' / getOption("max.print") -- omitted 1964 rows ]
DEAList_ips_AR
## $dds
## class: DESeqDataSet
## dim: 16616 6
## metadata(1): version
## assays(4): counts mu H cooks
## rownames(16616): TSPAN6 TNMD ... ZCCHC14-DT C8orf44
## rowData names(35): Gene EnsGene ... deviance maxCooks
## colnames(6): OLE_001 OLE_004 ... OLE_028 OLE_029
## colData names(12): SampleNumber SampleID_GU ... lib.size sizeFactor
##
## $AR
## $AR$res
## log2 fold change (MLE): Genotype AR vs WT
## Wald test p-value: Genotype AR vs WT
## DataFrame with 16616 rows and 6 columns
## baseMean log2FoldChange lfcSE stat pvalue padj
## <numeric> <numeric> <numeric> <numeric> <numeric> <numeric>
## TSPAN6 1589.535 -0.0550846 0.174872 -0.315000 0.752761 1
## TNMD 17.887 0.2107732 0.747061 0.282136 0.777839 1
## DPM1 906.561 -0.1257532 0.137613 -0.913819 0.360812 1
## SCYL3 154.222 -0.3003555 0.246447 -1.218744 0.222941 1
## C1orf112 648.142 0.1465394 0.163139 0.898250 0.369052 1
## ... ... ... ... ... ... ...
## DHX9-AS1 29.60314 -0.2629160 0.519740 -0.5058608 0.612954 1
## FAM106C 4.86974 -1.0198905 1.337371 -0.7626087 0.445697 1
## DUS4L-BCAP29 145.46191 0.0188132 0.258039 0.0729083 0.941879 1
## ZCCHC14-DT 3.39608 0.1693334 1.660320 0.1019885 0.918766 1
## C8orf44 65.41901 0.1318853 0.382319 0.3449614 0.730123 1
##
## $AR$DEGs
## baseMean log2FoldChange lfcSE stat pvalue padj
## ZNF506 282.22948 -1.1469872 0.2254824 -5.086816 3.641255e-07 3.559005e-04
## LRRC61 179.67569 -2.0922217 0.3163432 -6.613771 3.746522e-11 5.659291e-08
## TNNI3 132.34495 -1.6007541 0.3222102 -4.968044 6.763179e-07 6.243165e-04
## TFCP2 1310.51190 -0.9328431 0.1343744 -6.942121 3.862550e-12 8.022517e-09
## SLC15A4 115.23229 -5.1079818 0.5294291 -9.648095 5.007748e-22 2.080219e-18
## GLT1D1 35.04699 -8.5371005 1.5188848 -5.620637 1.902544e-08 2.107512e-05
## TMEM132D 28.11173 -8.5505683 1.5561545 -5.494678 3.914233e-08 4.064931e-05
## ZNF667-AS1 168.69830 -1.5483536 0.2713436 -5.706247 1.154944e-08 1.370753e-05
## PDE12 405.03599 -0.8485260 0.1923334 -4.411745 1.025407e-05 8.519085e-03
## TSPYL5 224.24750 1.5349468 0.2340561 6.558029 5.452348e-11 7.549685e-08
## LINC01551 56.26912 6.4736795 1.4578688 4.440509 8.974633e-06 7.848553e-03
## ZNF605 572.95301 -1.2157483 0.1815000 -6.698336 2.108059e-11 3.587438e-08
## ZFP28 130.64609 -1.2366492 0.2956687 -4.182551 2.882569e-05 2.082468e-02
## ZNF100 325.99274 -1.6916313 0.2170362 -7.794236 6.479953e-15 1.794515e-11
## ZNF667 256.97551 -1.5924777 0.2378663 -6.694843 2.159026e-11 3.587438e-08
## INPP5F 1225.87509 -1.7132772 0.1507428 -11.365567 6.206010e-30 5.155953e-26
## LINC00654 20.33855 -3.2974285 0.7662166 -4.303520 1.681058e-05 1.330117e-02
## SMIM11 120.22975 -3.8723953 0.4257387 -9.095710 9.397079e-20 3.122837e-16
## MEG3 5539.22335 -11.1894198 0.5122889 -21.842012 9.258705e-106 1.538426e-101
## MEG9 146.77233 -10.5026446 1.4680881 -7.153961 8.430919e-13 2.001259e-09
## MEG8 128.09806 -4.8573576 0.4586376 -10.590839 3.286326e-26 1.820187e-22
## LINC01515 35.93465 -5.7551523 0.9899801 -5.813402 6.121579e-09 7.824319e-06
## ZNF585B 234.21712 -1.1126851 0.2754908 -4.038919 5.369803e-05 3.692043e-02
## PABPC4L 92.75336 -1.3278578 0.3294148 -4.030960 5.554951e-05 3.692043e-02
## ZNF229 25.89545 -3.4262037 0.8155220 -4.201240 2.654570e-05 2.004924e-02
##
## $AR$resAshr
## log2 fold change (MMSE): Genotype AR vs WT
## Wald test p-value: Genotype AR vs WT
## DataFrame with 16616 rows and 5 columns
## baseMean log2FoldChange lfcSE pvalue padj
## <numeric> <numeric> <numeric> <numeric> <numeric>
## TSPAN6 1589.535 -0.000115952 0.00805291 0.752761 1
## TNMD 17.887 0.000125439 0.01870128 0.777839 1
## DPM1 906.561 -0.000417418 0.00810677 0.360812 1
## SCYL3 154.222 -0.000424422 0.01112184 0.222941 1
## C1orf112 648.142 0.000358484 0.00834297 0.369052 1
## ... ... ... ... ... ...
## DHX9-AS1 29.60314 -1.71831e-04 0.01425308 0.612954 1
## FAM106C 4.86974 -6.95825e-04 0.04097068 0.445697 1
## DUS4L-BCAP29 145.46191 2.09647e-05 0.00861825 0.941879 1
## ZCCHC14-DT 3.39608 9.31383e-05 0.03906130 0.918766 1
## C8orf44 65.41901 9.66827e-05 0.01060372 0.730123 1
##
## $AR$DEGsAshr
## baseMean log2FoldChange lfcSE pvalue padj
## ZNF506 282.22948 -1.1027582 0.2633438 3.641255e-07 3.559005e-04
## LRRC61 179.67569 -2.0245757 0.3160109 3.746522e-11 5.659291e-08
## TNNI3 132.34495 -1.4959925 0.3995629 6.763179e-07 6.243165e-04
## TFCP2 1310.51190 -0.9249087 0.1338903 3.862550e-12 8.022517e-09
## SLC15A4 115.23229 -5.0537930 0.5314937 5.007748e-22 2.080219e-18
## GLT1D1 35.04699 -7.9302563 1.5086247 1.902544e-08 2.107512e-05
## TMEM132D 28.11173 -7.9011221 1.5749680 3.914233e-08 4.064931e-05
## ZNF667-AS1 168.69830 -1.5021003 0.2716018 1.154944e-08 1.370753e-05
## PDE12 405.03599 -0.5874130 0.4123360 1.025407e-05 8.519085e-03
## TSPYL5 224.24750 1.5010568 0.2326347 5.452348e-11 7.549685e-08
## LINC01551 56.26912 4.2113983 2.9979915 8.974633e-06 7.848553e-03
## ZNF605 572.95301 -1.1980383 0.1805340 2.108059e-11 3.587438e-08
## ZFP28 130.64609 -0.6361358 0.6305834 2.882569e-05 2.082468e-02
## ZNF100 325.99274 -1.6609406 0.2161810 6.479953e-15 1.794515e-11
## ZNF667 256.97551 -1.5568135 0.2364974 2.159026e-11 3.587438e-08
## INPP5F 1225.87509 -1.6982290 0.1504768 6.206010e-30 5.155953e-26
## LINC00654 20.33855 -1.8452323 1.5928279 1.681058e-05 1.330117e-02
## SMIM11 120.22975 -3.8137804 0.4342392 9.397079e-20 3.122837e-16
## MEG3 5539.22335 -11.0961889 0.5101502 9.258705e-106 1.538426e-101
## MEG9 146.77233 -9.8246236 1.4200792 8.430919e-13 2.001259e-09
## MEG8 128.09806 -4.8156095 0.4610276 3.286326e-26 1.820187e-22
## LINC01515 35.93465 -5.5465185 1.0064504 6.121579e-09 7.824319e-06
## ZNF229 25.89545 -1.5906382 1.6720902 2.654570e-05 2.004924e-02DEA for Day25
DEAList_day25_HT <- readRDS(paste0(params$InputFolder, 'day25/Output/Savings/day25CbO.DEAList_HT.rds'))
DEAList_day25_AR <- readRDS(paste0(params$InputFolder, 'day25/Output/Savings/day25CbO.DEAList_AR.rds'))
DEAList_day25_HT
## $dds
## class: DESeqDataSet
## dim: 17781 13
## metadata(1): version
## assays(4): counts mu H cooks
## rownames(17781): TSPAN6 TNMD ... PDCD6-AHRR LNCDAT
## rowData names(51): Gene EnsGene ... deviance maxCooks
## colnames(13): OLE_007 OLE_008 ... OLE_038 OLE_039
## colData names(12): SampleNumber SampleID_GU ... lib.size sizeFactor
##
## $HT
## $HT$res
## log2 fold change (MLE): Genotype HT vs WT
## Wald test p-value: Genotype HT vs WT
## DataFrame with 17781 rows and 6 columns
## baseMean log2FoldChange lfcSE stat pvalue padj
## <numeric> <numeric> <numeric> <numeric> <numeric> <numeric>
## TSPAN6 1899.95350 0.126856 0.0916115 1.384712 0.1661405 0.416807
## TNMD 1.40474 -0.901158 1.7476042 -0.515653 0.6060966 NA
## DPM1 753.98864 -0.060679 0.0925993 -0.655286 0.5122838 0.757325
## SCYL3 324.26243 -0.123254 0.1218039 -1.011908 0.3115821 0.589861
## C1orf112 606.44497 -0.251886 0.0984460 -2.558627 0.0105086 0.061790
## ... ... ... ... ... ... ...
## C8orf44 219.88820 0.0784975 0.163767 0.479325 0.6317071 0.834864
## C8orf44-SGK3 6.72668 1.5490628 1.385756 1.117847 0.2636323 0.539837
## NPBWR1 3.20140 0.6146274 1.355148 0.453550 0.6501526 NA
## PDCD6-AHRR 25.30042 -3.7720161 3.456649 -1.091235 0.2751695 0.552450
## LNCDAT 7.67620 1.7878652 0.828398 2.158219 0.0309108 0.138228
##
## $HT$DEGs
## baseMean log2FoldChange lfcSE stat pvalue padj
## CFH 26.094947 3.0438007 0.86098471 3.535255 4.073815e-04 4.584685e-03
## ENPP4 218.503431 -0.9487343 0.21605496 -4.391171 1.127417e-05 2.172581e-04
## SEMA3F 718.820104 0.7659644 0.21251021 3.604365 3.129171e-04 3.703258e-03
## HS3ST1 120.628365 3.0725465 0.47583325 6.457192 1.066638e-10 6.740345e-09
## HECW1 127.870718 0.8530832 0.28992535 2.942424 3.256542e-03 2.508466e-02
## KLHL13 292.946998 -0.7107625 0.25499351 -2.787375 5.313699e-03 3.680034e-02
## CYP26B1 64.560436 2.0414678 0.48878717 4.176599 2.959004e-05 4.910949e-04
## SKAP2 67.788433 1.0430165 0.35508420 2.937378 3.310006e-03 2.542631e-02
## COPZ2 30.807971 -1.3257562 0.43865978 -3.022288 2.508717e-03 2.029516e-02
## GCFC2 327.213096 0.6547935 0.19298996 3.392889 6.915961e-04 7.131446e-03
## CRLF1 45.918894 4.5005324 0.88501633 5.085254 3.671353e-07 1.065520e-05
## TMEM132A 3163.250522 0.8947162 0.11032366 8.109921 5.065256e-16 7.068565e-14
## CACNA1G 822.061921 1.5438853 0.18415734 8.383512 5.137135e-17 8.039856e-15
## TNFRSF12A 425.539393 -0.8334366 0.24696415 -3.374727 7.388895e-04 7.525263e-03
## DNAH9 80.569116 1.7959513 0.44432183 4.042006 5.299596e-05 8.075254e-04
## GAS7 262.330977 1.8874426 0.35909060 5.256174 1.470833e-07 4.673733e-06
## TKTL1 88.388265 1.0787253 0.23269003 4.635890 3.554051e-06 7.962278e-05
## MYLIP 349.607378 1.1112255 0.29307916 3.791554 1.497075e-04 1.978691e-03
## SYN1 200.742500 -0.7202241 0.16252394 -4.431495 9.358188e-06 1.839345e-04
## CDKL5 497.681947 0.6214245 0.15060416 4.126211 3.687892e-05 5.938216e-04
## CAMK1G 91.022896 0.7867750 0.23961322 3.283521 1.025190e-03 9.771104e-03
## CELSR3 3297.631944 -0.7586497 0.15822476 -4.794760 1.628700e-06 4.034646e-05
## NFIX 30.513303 3.0083096 0.54844426 5.485169 4.130737e-08 1.516959e-06
## ST3GAL1 263.451894 0.8552380 0.19714822 4.338046 1.437552e-05 2.674806e-04
## MAPK8IP2 1703.933691 -0.7127392 0.15402096 -4.627547 3.700227e-06 8.261867e-05
## TENM1 526.238303 0.7691039 0.23466349 3.277476 1.047398e-03 9.937521e-03
## PAX7 2966.607755 0.8615305 0.13395539 6.431473 1.263729e-10 7.867067e-09
## SEMA3G 43.262789 2.9643450 0.66247272 4.474667 7.653036e-06 1.542211e-04
## CD4 86.746953 1.8461830 0.40334497 4.577181 4.712834e-06 1.014410e-04
## TSPAN9 992.198040 0.6073611 0.17847193 3.403119 6.662132e-04 6.903717e-03
## PLAUR 90.804887 3.2057038 0.34596076 9.266091 1.930935e-20 3.849457e-18
## DCN 568.463747 3.0202352 0.81595333 3.701480 2.143453e-04 2.656801e-03
## CLDN11 99.291097 -1.2250425 0.42240986 -2.900128 3.730106e-03 2.788587e-02
## MAMLD1 261.098025 1.2937545 0.17315493 7.471659 7.919022e-14 8.611165e-12
## MTMR11 147.270254 -0.6954796 0.25397624 -2.738365 6.174555e-03 4.137280e-02
## CCDC88C 1154.376702 1.2318640 0.16530258 7.452176 9.181304e-14 9.855776e-12
## BID 202.367418 0.9238731 0.22559114 4.095343 4.215433e-05 6.653313e-04
## WWTR1 1608.891689 1.2790136 0.19934825 6.415976 1.399234e-10 8.614549e-09
## ATP1A2 5466.677387 0.7011471 0.15398879 4.553235 5.282723e-06 1.117820e-04
## ZNF582 106.237060 -1.1563022 0.19672741 -5.877687 4.160376e-09 1.914002e-07
## PHLDB1 2326.554528 0.6739143 0.07190713 9.372008 7.116535e-21 1.453335e-18
## MARCO 20.098400 -2.4041912 0.84248337 -2.853696 4.321389e-03 3.139522e-02
## SNAI2 223.847963 1.6537623 0.42478656 3.893160 9.894665e-05 1.389391e-03
## CD74 101.752401 0.7251838 0.23339605 3.107095 1.889354e-03 1.612595e-02
## HGF 48.216629 7.3818414 1.62787017 4.534662 5.769574e-06 1.204704e-04
## ADGRA2 324.830161 3.5851638 0.56570418 6.337524 2.334869e-10 1.381615e-08
## RUNX3 6.872916 4.3332663 1.30237202 3.327211 8.771998e-04 8.646020e-03
## SERPINB1 51.905708 -0.8330960 0.30999969 -2.687409 7.200871e-03 4.658346e-02
## ABCC2 77.290170 1.9656992 0.48374511 4.063502 4.834192e-05 7.468024e-04
## FAS 150.275268 -1.1455279 0.26385194 -4.341556 1.414775e-05 2.641229e-04
## ARNTL2 174.888558 -0.9497172 0.27372988 -3.469542 5.213472e-04 5.643491e-03
## LRRC7 108.046025 -0.9442942 0.32537589 -2.902164 3.705946e-03 2.774556e-02
## APBA2 1686.739077 1.0059252 0.10281602 9.783739 1.322331e-22 3.209241e-20
## TMSB10 7552.547506 0.7227666 0.17218558 4.197603 2.697556e-05 4.562956e-04
## TLL1 12.651016 -1.9666972 0.71940567 -2.733781 6.261176e-03 4.177277e-02
## VCAN 15304.419355 1.0372404 0.20075009 5.166824 2.381054e-07 7.236501e-06
## RAI14 3657.542133 0.6989235 0.12558277 5.565441 2.614904e-08 1.013638e-06
## CDH10 433.931740 -0.9047519 0.15316677 -5.906972 3.484523e-09 1.620884e-07
## RIPOR3 16.756729 1.6037723 0.50664697 3.165463 1.548363e-03 1.371899e-02
## USH2A 57.012639 -1.3564541 0.48573894 -2.792558 5.229311e-03 3.630599e-02
## ARAP2 124.762877 -1.4244012 0.20776433 -6.855851 7.088939e-12 5.445476e-10
## LMO3 1129.207946 0.9787634 0.20766816 4.713113 2.439614e-06 5.786654e-05
## COL9A2 216.418926 0.7856526 0.24231844 3.242232 1.185975e-03 1.098470e-02
## ELN 343.750002 1.0419168 0.32486352 3.207245 1.340130e-03 1.215700e-02
## PPP1R3F 287.110950 -0.6087422 0.13676400 -4.451041 8.545510e-06 1.701583e-04
## COL23A1 299.891592 1.5286147 0.37891028 4.034239 5.477951e-05 8.309219e-04
## HOMER3 973.537438 0.6669470 0.08321356 8.014884 1.102414e-15 1.500896e-13
## ALX4 62.424694 3.7275951 0.58540511 6.367548 1.920741e-10 1.161182e-08
## LAMA3 51.721896 -1.3309408 0.47013709 -2.830963 4.640806e-03 3.328263e-02
## PHPT1 2017.187145 -0.6956466 0.09390555 -7.407939 1.282773e-13 1.309837e-11
## FOXC1 169.732191 0.9697764 0.31302112 3.098118 1.947537e-03 1.647144e-02
## PLEKHH1 456.598620 1.2480265 0.17167006 7.269913 3.597184e-13 3.442197e-11
## PARP12 65.279914 -0.9124330 0.29888380 -3.052802 2.267156e-03 1.868395e-02
## SLC2A3 1089.408979 -1.1424268 0.18184910 -6.282279 3.336449e-10 1.933293e-08
## PSD 918.925574 -0.7364148 0.15685285 -4.694940 2.666846e-06 6.205291e-05
## RIMBP2 339.775566 0.9608767 0.19299132 4.978860 6.396000e-07 1.755859e-05
## COL11A1 2620.885828 -0.8055683 0.13098350 -6.150151 7.740928e-10 4.102202e-08
## PRDM6 46.147992 -1.3272232 0.42458154 -3.125956 1.772281e-03 1.532195e-02
## GUCY1B1 359.307001 0.8520241 0.21507372 3.961545 7.446645e-05 1.084361e-03
## CDH3 115.083764 1.4311358 0.31809854 4.499033 6.826333e-06 1.404346e-04
## TM7SF3 1749.910744 -0.7496604 0.11327127 -6.618275 3.634148e-11 2.453929e-09
## NGFR 2329.716326 2.0779836 0.44023738 4.720143 2.356784e-06 5.606067e-05
## SNCAIP 260.170680 1.0266463 0.23739737 4.324590 1.528158e-05 2.815240e-04
## SLC9A3R2 65.870811 1.7960836 0.40511657 4.433498 9.271629e-06 1.826620e-04
## NTN1 121.905642 2.4032932 0.47150978 5.097017 3.450482e-07 1.004900e-05
## ERBB3 843.390203 4.6459828 0.64193307 7.237488 4.570716e-13 4.300068e-11
## ROPN1 12.544528 4.5740872 1.07475956 4.255917 2.081942e-05 3.646883e-04
## ANKRD44 306.039989 1.0254039 0.23424500 4.377485 1.200568e-05 2.295058e-04
## PRKCQ 41.457806 1.4665457 0.44802494 3.273357 1.062781e-03 1.007206e-02
## ME1 35.287912 -1.5880512 0.42333570 -3.751281 1.759333e-04 2.261074e-03
## CTNNA2 1875.110826 -0.8819497 0.18519362 -4.762312 1.913878e-06 4.658401e-05
## TIE1 95.688520 1.6811874 0.32979041 5.097745 3.437233e-07 1.002786e-05
## STAG3 76.435177 0.8939669 0.23021358 3.883206 1.030879e-04 1.436199e-03
## CBFB 1437.870064 0.6161926 0.11046607 5.578116 2.431371e-08 9.468775e-07
## LAPTM4A 1508.957366 0.8798920 0.22658032 3.883356 1.030246e-04 1.436199e-03
## TGFBR3 569.826299 0.6821606 0.21720243 3.140667 1.685634e-03 1.467132e-02
## FGF10 84.326946 -2.0245121 0.58208943 -3.478009 5.051536e-04 5.507359e-03
## ST6GALNAC2 5.409746 4.4177512 1.61194721 2.740630 6.132148e-03 4.117440e-02
## NCK2 1313.614599 0.6241392 0.08596429 7.260447 3.858123e-13 3.670916e-11
## LMCD1 140.988752 -0.8247264 0.16424137 -5.021429 5.128839e-07 1.441066e-05
## CDH19 185.249695 8.3458917 1.67515216 4.982169 6.287537e-07 1.731761e-05
## SLC6A15 587.038713 -0.6429582 0.21235197 -3.027795 2.463452e-03 1.999659e-02
## SPEG 600.513852 0.8828196 0.18699373 4.721119 2.345510e-06 5.587185e-05
## TRNT1 399.036066 -0.5891796 0.16030693 -3.675322 2.375492e-04 2.901531e-03
## STK10 305.451866 0.6122181 0.17315251 3.535716 4.066716e-04 4.579773e-03
## PANX2 85.288132 -1.1836661 0.27361299 -4.326060 1.518002e-05 2.799611e-04
## PTGS2 23.363877 4.4367382 0.88638888 5.005408 5.574376e-07 1.553220e-05
## MAP3K13 350.872641 -1.6218423 0.24247519 -6.688694 2.251716e-11 1.577709e-09
## ST6GAL1 946.031424 1.1716192 0.11050602 10.602312 2.907041e-26 8.540580e-24
## SEMA3C 917.956652 1.3113320 0.30492548 4.300500 1.704133e-05 3.095164e-04
## ZNF37A 212.146852 6.1642995 0.35274076 17.475438 2.204447e-68 4.101741e-65
## FSCN1 7818.193996 0.8229400 0.11900671 6.915072 4.676249e-12 3.642254e-10
## PAX2 295.741304 3.4855765 0.76673335 4.546009 5.467279e-06 1.147983e-04
## SLC46A1 163.629920 -0.8014018 0.22901770 -3.499301 4.664801e-04 5.156221e-03
## PAG1 795.875188 1.3442681 0.24552328 5.475115 4.372288e-08 1.584812e-06
## MCAM 275.226668 2.6124017 0.43289897 6.034668 1.592895e-09 7.845474e-08
## CTTNBP2 349.544411 1.1712458 0.24425943 4.795089 1.626023e-06 4.033982e-05
## CAPN6 39.711229 3.6216186 1.01180642 3.579359 3.444378e-04 4.005525e-03
## ITGA8 150.240069 1.9935254 0.43789049 4.552566 5.299552e-06 1.117820e-04
## SYNJ2 148.855847 -0.8343846 0.23869065 -3.495674 4.728664e-04 5.223364e-03
## ADCY2 691.221145 -0.6513854 0.18203195 -3.578412 3.456878e-04 4.017271e-03
## BRINP1 125.706735 1.6155204 0.25002670 6.461391 1.037445e-10 6.580705e-09
## RUNX1T1 290.240488 1.2433708 0.33783301 3.680430 2.328408e-04 2.850257e-03
## FKBP7 460.597114 0.8688453 0.15958166 5.444519 5.194566e-08 1.862702e-06
## TNS1 652.603607 1.4915821 0.27164102 5.491005 3.996538e-08 1.474141e-06
## MOXD1 932.633094 2.7412323 0.76214017 3.596756 3.222104e-04 3.794469e-03
## DCT 59.062425 0.8596046 0.27927388 3.077999 2.083959e-03 1.742285e-02
## SESN1 941.182511 -1.2002453 0.17017468 -7.053019 1.750767e-12 1.503505e-10
## COL5A3 102.867590 3.3585265 0.54074259 6.210952 5.266440e-10 2.920258e-08
## MEF2C 239.182267 1.2817884 0.37327671 3.433882 5.950021e-04 6.310263e-03
## AACS 560.420968 0.6859040 0.12957774 5.293378 1.200773e-07 3.945769e-06
## PCDHA6 249.677359 4.6732955 0.21853234 21.384915 1.846248e-101 1.030576e-97
## SERTAD4 389.392252 1.3098770 0.25199420 5.198045 2.013959e-07 6.233967e-06
## OPRK1 48.580938 -1.4590153 0.46120667 -3.163474 1.558983e-03 1.378391e-02
## LYRM2 1131.131783 -1.0249882 0.08361564 -12.258331 1.515895e-34 7.051436e-32
## SLC27A5 85.311999 -0.7216511 0.21425030 -3.368262 7.564374e-04 7.669595e-03
## FAM234B 495.856221 -0.6176869 0.10503019 -5.881042 4.076929e-09 1.891198e-07
## SLCO1A2 100.222222 2.9006897 0.39031546 7.431655 1.072475e-13 1.136688e-11
## NKAIN1 1420.368524 1.0787586 0.16219745 6.650897 2.913113e-11 1.999303e-09
## COL16A1 100.782242 1.9727019 0.62628293 3.149857 1.633502e-03 1.429933e-02
## EFR3B 1670.269246 0.5882143 0.12852987 4.576480 4.728652e-06 1.016509e-04
## PREP 897.889194 0.5984011 0.14781693 4.048258 5.160016e-05 7.892399e-04
## ABCB1 86.830515 -1.8460473 0.57134914 -3.231032 1.233442e-03 1.133034e-02
## WNT11 29.349678 2.2819322 0.52777193 4.323709 1.534277e-05 2.823406e-04
## PPEF1 37.653044 1.8522545 0.51834470 3.573403 3.523719e-04 4.080788e-03
## BAX 1038.927079 -0.9168254 0.13620937 -6.731001 1.684999e-11 1.232183e-09
## ADAMTS2 214.063991 1.3983249 0.18052160 7.746025 9.481367e-15 1.142266e-12
## MMP2 2109.069578 1.1129752 0.16063063 6.928786 4.244686e-12 3.352901e-10
## GNAO1 1183.611230 -0.9323370 0.27333493 -3.410969 6.473247e-04 6.753956e-03
## SH3BP2 1203.121984 0.7137084 0.12368230 5.770497 7.903810e-09 3.428943e-07
## NID2 202.360977 2.3530468 0.44102439 5.335412 9.532791e-08 3.238055e-06
## PHACTR3 115.215407 1.1253445 0.37658951 2.988252 2.805776e-03 2.231032e-02
## TFAP2C 78.284764 4.2074733 1.00203121 4.198944 2.681622e-05 4.545186e-04
## DOCK9 194.313627 0.6715095 0.21653363 3.101179 1.927520e-03 1.632695e-02
## C3orf18 145.755327 -0.6280050 0.20965484 -2.995424 2.740640e-03 2.190681e-02
## ARHGAP28 720.983385 1.1497726 0.26298196 4.372059 1.230803e-05 2.342162e-04
## SMOX 291.626581 0.8708279 0.22848598 3.811297 1.382395e-04 1.853450e-03
## SLC4A11 42.453434 -0.8773281 0.30216221 -2.903500 3.690166e-03 2.767213e-02
## FXYD5 51.429416 1.5641153 0.48792156 3.205670 1.347486e-03 1.220390e-02
## PITPNM2 283.322341 -0.7924381 0.12546570 -6.315973 2.684662e-10 1.571935e-08
## LAMB1 1886.846162 2.4071061 0.46865253 5.136228 2.803081e-07 8.352384e-06
## CCDC80 1509.048047 -1.6637058 0.24371984 -6.826304 8.713002e-12 6.662463e-10
## WDR76 478.334624 -0.8356596 0.22367225 -3.736090 1.869038e-04 2.378337e-03
## CAPN3 44.501543 0.8687641 0.31421288 2.764890 5.694195e-03 3.885697e-02
## TBX15 72.509651 2.7047557 0.56373371 4.797931 1.603126e-06 3.988998e-05
## COL9A3 242.331908 2.3793395 0.35512495 6.700007 2.084103e-11 1.480981e-09
## [ reached 'max' / getOption("max.print") -- omitted 1345 rows ]
##
## $HT$resAshr
## log2 fold change (MMSE): Genotype HT vs WT
## Wald test p-value: Genotype HT vs WT
## DataFrame with 17781 rows and 5 columns
## baseMean log2FoldChange lfcSE pvalue padj
## <numeric> <numeric> <numeric> <numeric> <numeric>
## TSPAN6 1899.95350 0.0661316 0.0759612 0.1661405 0.416807
## TNMD 1.40474 -0.0348380 0.3563090 0.6060966 NA
## DPM1 753.98864 -0.0273858 0.0649198 0.5122838 0.757325
## SCYL3 324.26243 -0.0504830 0.0852623 0.3115821 0.589861
## C1orf112 606.44497 -0.1677184 0.1002672 0.0105086 0.061790
## ... ... ... ... ... ...
## C8orf44 219.88820 0.0241253 0.092974 0.6317071 0.834864
## C8orf44-SGK3 6.72668 0.0894832 0.394144 0.2636323 0.539837
## NPBWR1 3.20140 0.0309958 0.313306 0.6501526 NA
## PDCD6-AHRR 25.30042 -0.0752447 0.566431 0.2751695 0.552450
## LNCDAT 7.67620 0.3241569 0.589033 0.0309108 0.138228
##
## $HT$DEGsAshr
## baseMean log2FoldChange lfcSE pvalue padj
## CFH 26.094947 1.8204589 1.20690149 4.073815e-04 4.584685e-03
## ENPP4 218.503431 -0.8351669 0.23132770 1.127417e-05 2.172581e-04
## SEMA3F 718.820104 0.6111376 0.25208213 3.129171e-04 3.703258e-03
## HS3ST1 120.628365 2.8755673 0.49877068 1.066638e-10 6.740345e-09
## CYP26B1 64.560436 1.6690993 0.56624201 2.959004e-05 4.910949e-04
## SKAP2 67.788433 0.5908787 0.43681468 3.310006e-03 2.542631e-02
## COPZ2 30.807971 -0.7332842 0.55007598 2.508717e-03 2.029516e-02
## CRLF1 45.918894 4.0226092 0.96985366 3.671353e-07 1.065520e-05
## TMEM132A 3163.250522 0.8672252 0.11105665 5.065256e-16 7.068565e-14
## CACNA1G 822.061921 1.4933118 0.18716908 5.137135e-17 8.039856e-15
## TNFRSF12A 425.539393 -0.6173661 0.30199339 7.388895e-04 7.525263e-03
## DNAH9 80.569116 1.4485745 0.52139554 5.299596e-05 8.075254e-04
## GAS7 262.330977 1.7067523 0.37643787 1.470833e-07 4.673733e-06
## TKTL1 88.388265 0.9598199 0.24567400 3.554051e-06 7.962278e-05
## MYLIP 349.607378 0.8910395 0.34283487 1.497075e-04 1.978691e-03
## SYN1 200.742500 -0.6452231 0.17476732 9.358188e-06 1.839345e-04
## CELSR3 3297.631944 -0.6933477 0.16543633 1.628700e-06 4.034646e-05
## NFIX 30.513303 2.7266283 0.58613440 4.130737e-08 1.516959e-06
## ST3GAL1 263.451894 0.7542074 0.21215554 1.437552e-05 2.674806e-04
## MAPK8IP2 1703.933691 -0.6470743 0.16330372 3.700227e-06 8.261867e-05
## PAX7 2966.607755 0.8200388 0.13540494 1.263729e-10 7.867067e-09
## SEMA3G 43.262789 2.4864249 0.76617647 7.653036e-06 1.542211e-04
## CD4 86.746953 1.5982950 0.43935052 4.712834e-06 1.014410e-04
## PLAUR 90.804887 3.1141296 0.35404172 1.930935e-20 3.849457e-18
## DCN 568.463747 2.0128626 1.12462857 2.143453e-04 2.656801e-03
## CLDN11 99.291097 -0.6366996 0.51610088 3.730106e-03 2.788587e-02
## MAMLD1 261.098025 1.2403644 0.17667022 7.919022e-14 8.611165e-12
## CCDC88C 1154.376702 1.1810600 0.16842548 9.181304e-14 9.855776e-12
## BID 202.367418 0.7907721 0.24950829 4.215433e-05 6.653313e-04
## WWTR1 1608.891689 1.2063943 0.20466736 1.399234e-10 8.614549e-09
## ATP1A2 5466.677387 0.6339970 0.16433042 5.282723e-06 1.117820e-04
## ZNF582 106.237060 -1.0791550 0.20192369 4.160376e-09 1.914002e-07
## PHLDB1 2326.554528 0.6611069 0.07213194 7.116535e-21 1.453335e-18
## MARCO 20.098400 -0.8193686 0.95328420 4.321389e-03 3.139522e-02
## SNAI2 223.847963 1.3021122 0.50868468 9.894665e-05 1.389391e-03
## HGF 48.216629 6.0858591 1.96992360 5.769574e-06 1.204704e-04
## ADGRA2 324.830161 3.3569809 0.59455300 2.334869e-10 1.381615e-08
## RUNX3 6.872916 1.8359420 1.82162316 8.771998e-04 8.646020e-03
## ABCC2 77.290170 1.5786640 0.57048606 4.834192e-05 7.468024e-04
## FAS 150.275268 -0.9925455 0.28619963 1.414775e-05 2.641229e-04
## ARNTL2 174.888558 -0.7129411 0.33315937 5.213472e-04 5.643491e-03
## APBA2 1686.739077 0.9834384 0.10348487 1.322331e-22 3.209241e-20
## TMSB10 7552.547506 0.6345593 0.18932762 2.697556e-05 4.562956e-04
## TLL1 12.651016 -0.6706594 0.78335163 6.261176e-03 4.177277e-02
## VCAN 15304.419355 0.9497228 0.20710314 2.381054e-07 7.236501e-06
## RAI14 3657.542133 0.6583681 0.12842594 2.614904e-08 1.013638e-06
## CDH10 433.931740 -0.8512471 0.15552753 3.484523e-09 1.620884e-07
## RIPOR3 16.756729 0.9179563 0.65243692 1.548363e-03 1.371899e-02
## USH2A 57.012639 -0.6146691 0.57150844 5.229311e-03 3.630599e-02
## ARAP2 124.762877 -1.3532752 0.21314720 7.088939e-12 5.445476e-10
## LMO3 1129.207946 0.8794423 0.21743646 2.439614e-06 5.786654e-05
## ELN 343.750002 0.6919265 0.40693564 1.340130e-03 1.215700e-02
## COL23A1 299.891592 1.2484701 0.43864340 5.477951e-05 8.309219e-04
## HOMER3 973.537438 0.6496463 0.08363206 1.102414e-15 1.500896e-13
## ALX4 62.424694 3.4955547 0.61405445 1.920741e-10 1.161182e-08
## LAMA3 51.721896 -0.6299780 0.56155278 4.640806e-03 3.328263e-02
## PHPT1 2017.187145 -0.6738356 0.09449508 1.282773e-13 1.309837e-11
## FOXC1 169.732191 0.6189686 0.39024906 1.947537e-03 1.647144e-02
## PLEKHH1 456.598620 1.1937296 0.17514620 3.597184e-13 3.442197e-11
## SLC2A3 1089.408979 -1.0763779 0.18590339 3.336449e-10 1.933293e-08
## PSD 918.925574 -0.6703328 0.16521941 2.666846e-06 6.205291e-05
## RIMBP2 339.775566 0.8758933 0.19963762 6.396000e-07 1.755859e-05
## COL11A1 2620.885828 -0.7647290 0.13254546 7.740928e-10 4.102202e-08
## PRDM6 46.147992 -0.7883202 0.53931473 1.772281e-03 1.532195e-02
## GUCY1B1 359.307001 0.7206140 0.24218923 7.446645e-05 1.084361e-03
## CDH3 115.083764 1.2443502 0.34532395 6.826333e-06 1.404346e-04
## TM7SF3 1749.910744 -0.7185034 0.11429207 3.634148e-11 2.453929e-09
## NGFR 2329.716326 1.8108795 0.47550455 2.356784e-06 5.606067e-05
## SNCAIP 260.170680 0.8940764 0.25639396 1.528158e-05 2.815240e-04
## SLC9A3R2 65.870811 1.5349417 0.44752509 9.271629e-06 1.826620e-04
## NTN1 121.905642 2.1378001 0.50141293 3.450482e-07 1.004900e-05
## ERBB3 843.390203 4.4347840 0.65837102 4.570716e-13 4.300068e-11
## ROPN1 12.544528 3.6582079 1.38966794 2.081942e-05 3.646883e-04
## ANKRD44 306.039989 0.8973202 0.25167882 1.200568e-05 2.295058e-04
## PRKCQ 41.457806 0.9258806 0.57631846 1.062781e-03 1.007206e-02
## ME1 35.287912 -1.2100403 0.51861987 1.759333e-04 2.261074e-03
## CTNNA2 1875.110826 -0.7989689 0.19316099 1.913878e-06 4.658401e-05
## TIE1 95.688520 1.5137529 0.34776511 3.437233e-07 1.002786e-05
## STAG3 76.435177 0.7442613 0.26232508 1.030879e-04 1.436199e-03
## LAPTM4A 1508.957366 0.7335021 0.25812226 1.030246e-04 1.436199e-03
## FGF10 84.326946 -1.3137151 0.76715974 5.051536e-04 5.507359e-03
## ST6GALNAC2 5.409746 0.7703031 1.42114751 6.132148e-03 4.117440e-02
## NCK2 1313.614599 0.6050463 0.08671326 3.858123e-13 3.670916e-11
## LMCD1 140.988752 -0.7586322 0.16953054 5.128839e-07 1.441066e-05
## CDH19 185.249695 7.1952215 1.78966970 6.287537e-07 1.731761e-05
## SPEG 600.513852 0.7979340 0.19546694 2.345510e-06 5.587185e-05
## PANX2 85.288132 -1.0220999 0.29793286 1.518002e-05 2.799611e-04
## PTGS2 23.363877 3.9432427 0.97911467 5.574376e-07 1.553220e-05
## MAP3K13 350.872641 -1.5349610 0.24883485 2.251716e-11 1.577709e-09
## ST6GAL1 946.031424 1.1483420 0.11147459 2.907041e-26 8.540580e-24
## SEMA3C 917.956652 1.1228890 0.33554589 1.704133e-05 3.095164e-04
## ZNF37A 212.146852 6.1169572 0.35362701 2.204447e-68 4.101741e-65
## FSCN1 7818.193996 0.7897505 0.11997776 4.676249e-12 3.642254e-10
## PAX2 295.741304 2.9507472 0.89484931 5.467279e-06 1.147983e-04
## SLC46A1 163.629920 -0.6198474 0.27568570 4.664801e-04 5.156221e-03
## PAG1 795.875188 1.2358462 0.25531771 4.372288e-08 1.584812e-06
## MCAM 275.226668 2.4134143 0.45148804 1.592895e-09 7.845474e-08
## CTTNBP2 349.544411 1.0484293 0.25692016 1.626023e-06 4.033982e-05
## CAPN6 39.711229 2.1303538 1.46250565 3.444378e-04 4.005525e-03
## ITGA8 150.240069 1.7149465 0.47957243 5.299552e-06 1.117820e-04
## SYNJ2 148.855847 -0.6418755 0.28779687 4.728664e-04 5.223364e-03
## BRINP1 125.706735 1.5222507 0.25718006 1.037445e-10 6.580705e-09
## RUNX1T1 290.240488 0.9581089 0.40736905 2.328408e-04 2.850257e-03
## FKBP7 460.597114 0.8091182 0.16289516 5.194566e-08 1.862702e-06
## TNS1 652.603607 1.3697167 0.28326789 3.996538e-08 1.474141e-06
## MOXD1 932.633094 1.7574235 1.04337171 3.222104e-04 3.794469e-03
## SESN1 941.182511 -1.1450055 0.17356136 1.750767e-12 1.503505e-10
## COL5A3 102.867590 3.1297734 0.57024997 5.266440e-10 2.920258e-08
## MEF2C 239.182267 0.9037346 0.46872195 5.950021e-04 6.310263e-03
## AACS 560.420968 0.6415484 0.13357424 1.200773e-07 3.945769e-06
## PCDHA6 249.677359 4.6503431 0.21899197 1.846248e-101 1.030576e-97
## SERTAD4 389.392252 1.1919451 0.26321914 2.013959e-07 6.233967e-06
## OPRK1 48.580938 -0.8615249 0.59078709 1.558983e-03 1.378391e-02
## LYRM2 1131.131783 -1.0103273 0.08398768 1.515895e-34 7.051436e-32
## FAM234B 495.856221 -0.5877389 0.10752818 4.076929e-09 1.891198e-07
## SLCO1A2 100.222222 2.7616542 0.40367926 1.072475e-13 1.136688e-11
## NKAIN1 1420.368524 1.0243981 0.16498503 2.913113e-11 1.999303e-09
## COL16A1 100.782242 1.0261519 0.81043549 1.633502e-03 1.429933e-02
## ABCB1 86.830515 -1.0520829 0.74611367 1.233442e-03 1.133034e-02
## WNT11 29.349678 1.8942069 0.60286471 1.534277e-05 2.823406e-04
## PPEF1 37.653044 1.2883648 0.66781463 3.523719e-04 4.080788e-03
## BAX 1038.927079 -0.8751035 0.13768150 1.684999e-11 1.232183e-09
## ADAMTS2 214.063991 1.3445415 0.18416067 9.481367e-15 1.142266e-12
## MMP2 2109.069578 1.0608657 0.16339637 4.244686e-12 3.352901e-10
## GNAO1 1183.611230 -0.6881921 0.33474421 6.473247e-04 6.753956e-03
## SH3BP2 1203.121984 0.6751120 0.12590180 7.903810e-09 3.428943e-07
## NID2 202.360977 2.1206132 0.46378080 9.532791e-08 3.238055e-06
## PHACTR3 115.215407 0.6435296 0.46771759 2.805776e-03 2.231032e-02
## TFAP2C 78.284764 3.3232530 1.30405015 2.681622e-05 4.545186e-04
## ARHGAP28 720.983385 0.9988736 0.28446912 1.230803e-05 2.342162e-04
## SMOX 291.626581 0.7175695 0.26314324 1.382395e-04 1.853450e-03
## FXYD5 51.429416 0.9283993 0.62954563 1.347486e-03 1.220390e-02
## PITPNM2 283.322341 -0.7548270 0.12680947 2.684662e-10 1.571935e-08
## LAMB1 1886.846162 2.1459243 0.49751556 2.803081e-07 8.352384e-06
## CCDC80 1509.048047 -1.5780054 0.24964565 8.713002e-12 6.662463e-10
## WDR76 478.334624 -0.6811357 0.26046380 1.869038e-04 2.378337e-03
## TBX15 72.509651 2.3508271 0.61864600 1.603126e-06 3.988998e-05
## COL9A3 242.331908 2.2361190 0.36464302 2.084103e-11 1.480981e-09
## COMT 452.481912 -5.9653802 0.37944297 4.504574e-57 6.857599e-54
## MAP3K1 1148.013026 0.6874149 0.18612274 9.461281e-06 1.855253e-04
## PTGS1 31.509437 1.1099582 0.48366641 2.144986e-04 2.656801e-03
## CYP26A1 98.213130 -0.8634663 0.78255964 2.843182e-03 2.254352e-02
## SORBS1 909.124977 1.6123366 0.21944433 7.402449e-15 9.114809e-13
## MYO3A 557.286642 -0.5931849 0.13312794 5.000475e-07 1.412107e-05
## ITPR3 189.684498 1.3142699 0.41928637 2.504339e-05 4.274990e-04
## DSP 380.546181 0.7302231 0.65140214 3.668967e-03 2.753946e-02
## PCSK5 244.525493 0.6110098 0.29325472 6.836661e-04 7.071253e-03
## MADCAM1 54.581374 1.1979226 0.31208287 3.240233e-06 7.370437e-05
## P2RX6 137.787116 0.5925481 0.26607335 5.057900e-04 5.508873e-03
## MFNG 267.898872 0.7451119 0.40427475 9.140961e-04 8.946495e-03
## LGALS1 193.581100 2.0250769 0.56389737 4.013803e-06 8.774823e-05
## SOX10 483.139150 6.3790203 1.41654487 1.289535e-07 4.168831e-06
## TIMP3 871.015109 1.8614504 0.54559831 7.704417e-06 1.550699e-04
## IL2RB 13.660909 2.1325269 1.25430852 2.280388e-04 2.795561e-03
## MLC1 44.178387 -0.8112794 0.48961928 1.173473e-03 1.089905e-02
## RIN3 141.716968 0.6028604 0.31142311 9.582589e-04 9.269053e-03
## SIX4 251.213438 0.7907314 0.22251487 1.404329e-05 2.630526e-04
## DHRS2 54.781227 1.2420834 0.33526578 4.903932e-06 1.048142e-04
## NFATC2 79.980931 2.9494065 0.48055909 1.090948e-11 8.266520e-10
## BMP7 1638.740410 0.9727772 0.17291140 1.110669e-09 5.636143e-08
## CTSZ 190.448842 -1.2491211 0.35751619 9.584436e-06 1.877204e-04
## SLCO4A1 37.472438 0.8858873 0.44832350 5.564887e-04 5.962226e-03
## COL20A1 31.422993 3.3312918 0.61835071 9.796481e-10 5.063329e-08
## CHRNA4 296.314528 0.7991794 0.28413775 1.029810e-04 1.436199e-03
## ISM1 63.701681 1.0153693 0.63243987 9.245800e-04 9.012233e-03
## PDYN 26.279039 0.7820848 0.56489018 2.069371e-03 1.733551e-02
## PLCB4 705.393857 0.9261918 0.24646436 6.231323e-06 1.291457e-04
## MYL9 37.302147 -1.5761753 0.49775004 1.857695e-05 3.323607e-04
## MROH8 78.954114 -0.6126304 0.25303087 3.148616e-04 3.720055e-03
## SNTA1 166.797244 -0.5888797 0.17224662 2.130902e-05 3.717093e-04
## SYP 836.231919 -0.9039093 0.17559993 1.755877e-08 7.051298e-07
## ASB9 6.741230 1.5457888 1.74469868 1.365990e-03 1.233255e-02
## PCYT1B 160.992279 0.6371812 0.37885514 1.543869e-03 1.368641e-02
## TIMP1 445.231612 -0.8863550 0.35883069 2.001202e-04 2.514038e-03
## KLHL4 262.136971 -0.7557330 0.27356375 1.220067e-04 1.657034e-03
## SYTL4 20.803237 -0.8662000 0.65733687 1.987567e-03 1.675921e-02
## RUBCNL 82.459803 1.6509604 0.32246393 9.038271e-09 3.880895e-07
## ACP5 6.852640 1.0745801 1.29709462 2.725655e-03 2.179743e-02
## FGF9 328.553077 0.6466550 0.24839585 1.980994e-04 2.494265e-03
## FLT1 58.806278 -1.1250030 0.39891352 6.668891e-05 9.848082e-04
## MAPK3 948.417335 -1.0533247 0.09279005 3.892485e-31 1.481444e-28
## GDPD3 45.518635 -1.2023284 0.30377389 2.089265e-06 5.012440e-05
## CRISPLD2 73.086545 1.7311632 0.42183952 8.564777e-07 2.258469e-05
## CRYM 68.163353 0.8993002 0.63481968 1.572293e-03 1.387961e-02
## SLC6A2 10.232749 1.5828511 1.18970999 6.886514e-04 7.105457e-03
## AP3B2 1357.167977 -0.7848479 0.12349956 2.091538e-11 1.480981e-09
## CTSH 74.155863 -1.1046362 0.23612722 1.158029e-07 3.824923e-06
## BMF 1449.952680 0.9945312 0.13813956 3.679141e-14 4.249027e-12
## TRPA1 11.226665 0.9709660 0.85960104 2.224268e-03 1.841206e-02
## CPQ 27.090485 -0.5914849 0.47881376 4.147806e-03 3.037130e-02
## CALB1 737.727904 -2.3041071 0.24338084 7.334321e-23 1.806184e-20
## SFRP1 1447.047551 0.6865710 0.25593851 1.582987e-04 2.068083e-03
## NIPAL2 32.799299 -0.6766169 0.52283634 3.043752e-03 2.383387e-02
## PLAT 345.386781 1.1213317 0.36062456 3.267704e-05 5.333428e-04
## GSDMD 34.351513 -2.9197826 0.39464009 1.775085e-15 2.378046e-13
## OLFM2 334.559507 0.9191335 0.23977827 4.882146e-06 1.046817e-04
## SLC1A6 183.532876 0.9616731 0.26051185 7.364988e-06 1.494959e-04
## KCNN1 195.412604 0.8760081 0.29538848 6.450009e-05 9.567037e-04
## TFPI2 192.192277 -2.3096581 0.38878050 6.071385e-11 3.987114e-09
## DLX5 6.841212 1.3995296 1.64847563 1.686596e-03 1.467207e-02
## [ reached 'max' / getOption("max.print") -- omitted 1037 rows ]
DEAList_day25_AR
## $dds
## class: DESeqDataSet
## dim: 17781 13
## metadata(1): version
## assays(4): counts mu H cooks
## rownames(17781): TSPAN6 TNMD ... PDCD6-AHRR LNCDAT
## rowData names(51): Gene EnsGene ... deviance maxCooks
## colnames(13): OLE_007 OLE_008 ... OLE_038 OLE_039
## colData names(12): SampleNumber SampleID_GU ... lib.size sizeFactor
##
## $AR
## $AR$res
## log2 fold change (MLE): Genotype AR vs WT
## Wald test p-value: Genotype AR vs WT
## DataFrame with 17781 rows and 6 columns
## baseMean log2FoldChange lfcSE stat pvalue padj
## <numeric> <numeric> <numeric> <numeric> <numeric> <numeric>
## TSPAN6 1899.95350 -0.00321804 0.107759 -0.0298632 0.97617617 0.9969430
## TNMD 1.40474 -2.67322743 2.191542 -1.2197928 0.22254342 NA
## DPM1 753.98864 -0.12588099 0.109614 -1.1484013 0.25080293 0.7661892
## SCYL3 324.26243 -0.10145290 0.143237 -0.7082863 0.47876749 0.8878547
## C1orf112 606.44497 -0.37363020 0.115953 -3.2222548 0.00127186 0.0876281
## ... ... ... ... ... ... ...
## C8orf44 219.88820 0.164147 0.192447 0.852950 0.393687 0.848049
## C8orf44-SGK3 6.72668 0.282797 1.577018 0.179324 0.857683 0.981561
## NPBWR1 3.20140 0.428658 1.613866 0.265609 0.790540 NA
## PDCD6-AHRR 25.30042 -2.044981 4.131004 -0.495033 0.620577 0.938008
## LNCDAT 7.67620 -0.939696 1.016744 -0.924221 0.355371 0.825025
##
## $AR$DEGs
## baseMean log2FoldChange lfcSE stat pvalue padj
## ZMYND10 57.19480 1.3624567 0.3892638 3.500086 4.651089e-04 4.624891e-02
## CACNA1G 822.06192 0.7856551 0.2171074 3.618739 2.960425e-04 3.493302e-02
## NRXN3 125.92310 1.5316628 0.3828391 4.000800 6.312865e-05 1.247513e-02
## DSG2 537.93484 1.3351256 0.3360632 3.972840 7.102070e-05 1.354513e-02
## UBE2T 701.97049 -1.0105319 0.1132986 -8.919190 4.697111e-19 1.284034e-15
## OSBPL6 248.89844 -0.6141677 0.1721876 -3.566851 3.612962e-04 4.027025e-02
## ZNF506 590.46712 -1.0754446 0.1436865 -7.484663 7.173113e-14 1.593125e-10
## ZNF671 204.82774 -1.0215515 0.2865220 -3.565351 3.633701e-04 4.027025e-02
## HSD17B14 169.46894 1.0153134 0.2645589 3.837760 1.241619e-04 2.036503e-02
## BMP7 1638.74041 0.9745700 0.2000345 4.872011 1.104683e-06 4.897028e-04
## PGK1 6036.99928 -0.6464248 0.1565218 -4.129935 3.628658e-05 8.153048e-03
## GPR50 107.23642 1.9081133 0.4578166 4.167855 3.074789e-05 7.120976e-03
## BMF 1449.95268 0.6081731 0.1599923 3.801265 1.439591e-04 2.166254e-02
## UNC5B 725.91188 1.2470010 0.2708843 4.603446 4.155569e-06 1.585108e-03
## FZD10 1452.12492 -5.8717934 0.6206858 -9.460170 3.074433e-21 1.260671e-17
## RND3 2668.94662 -1.0237312 0.2790252 -3.668956 2.435428e-04 3.072761e-02
## CLU 2438.39969 0.9569952 0.1931230 4.955366 7.219434e-07 3.383233e-04
## DNAI1 85.97086 0.7937699 0.2272564 3.492839 4.779154e-04 4.693873e-02
## EGR2 183.81068 -1.6163152 0.3922085 -4.121062 3.771305e-05 8.359047e-03
## P4HA1 1803.85468 -0.9187165 0.1918919 -4.787678 1.687221e-06 7.095845e-04
## SSUH2 70.59441 -2.2201533 0.3843751 -5.776007 7.649401e-09 5.702976e-06
## APOE 335.84670 1.6050037 0.4165763 3.852845 1.167535e-04 1.982363e-02
## SPINK5 338.95977 1.3031693 0.3127142 4.167285 3.082486e-05 7.120976e-03
## LMO2 173.60297 2.3075551 0.5840546 3.950923 7.785024e-05 1.451022e-02
## TFCP2 1320.40127 -0.7005710 0.1067600 -6.562109 5.305196e-11 5.438489e-08
## ZFHX2 692.36492 0.6727438 0.1739719 3.866968 1.101968e-04 1.902577e-02
## SPAG8 109.41046 1.0721469 0.2389824 4.486301 7.247021e-06 2.330699e-03
## MNS1 149.14792 -0.8892892 0.2355938 -3.774671 1.602192e-04 2.367492e-02
## LEF1 857.44881 0.9722526 0.2766127 3.514852 4.399992e-04 4.510542e-02
## SLC15A4 124.41296 -4.0253318 0.3978958 -10.116547 4.665860e-24 2.550981e-20
## HDC 57.64489 3.1183735 0.8561961 3.642125 2.703965e-04 3.273311e-02
## CFAP74 57.33016 2.0365413 0.4534864 4.490855 7.093796e-06 2.327049e-03
## RSPO3 346.42227 1.4587272 0.3523141 4.140416 3.466762e-05 7.897476e-03
## TRIM4 168.68946 1.7859980 0.4533840 3.939261 8.173298e-05 1.506275e-02
## IGSF1 215.36251 1.3773355 0.3938709 3.496921 4.706611e-04 4.650472e-02
## VAX1 72.91832 4.6506944 1.0901135 4.266248 1.987878e-05 5.284352e-03
## LRRC4C 121.95019 1.4394951 0.3670378 3.921926 8.784400e-05 1.583316e-02
## GLT1D1 35.03359 -6.4608763 1.2769046 -5.059796 4.197058e-07 2.024710e-04
## TMEM132D 168.74525 -9.3104298 1.2673318 -7.346482 2.034921e-13 2.781399e-10
## ANGPT1 55.85853 -2.2887429 0.4112982 -5.564680 2.626337e-08 1.794882e-05
## GRIA1 1958.45414 -0.7809598 0.2096796 -3.724538 1.956732e-04 2.662048e-02
## B3GNT7 38.35613 1.6018271 0.4039281 3.965624 7.320411e-05 1.380108e-02
## TMSB15B 275.74392 -0.7978565 0.1857422 -4.295505 1.742958e-05 4.845423e-03
## TPPP3 102.76556 1.4693725 0.3687899 3.984308 6.767717e-05 1.321477e-02
## RSPH1 47.87268 1.9430801 0.5208508 3.730589 1.910329e-04 2.655357e-02
## PPP1R32 135.35555 0.9363681 0.2052502 4.562081 5.064903e-06 1.767543e-03
## ABHD6 157.40356 0.9937770 0.2727153 3.644008 2.684248e-04 3.273311e-02
## SERINC5 685.24965 1.0467354 0.2938921 3.561632 3.685574e-04 4.042342e-02
## IFTAP 169.11163 4.2197834 0.5678572 7.431064 1.077277e-13 1.766949e-10
## CRABP1 12001.80107 -1.2840464 0.2808614 -4.571815 4.835183e-06 1.724058e-03
## ZNF667-AS1 234.54796 -1.4857642 0.2558097 -5.808083 6.319222e-09 4.935614e-06
## ZNF558 27.67133 -5.6794358 1.2352324 -4.597868 4.268358e-06 1.591128e-03
## PFKFB3 953.14539 -0.6080256 0.1433679 -4.241017 2.225092e-05 5.614764e-03
## ZNF439 325.88711 -0.8919666 0.2003838 -4.451290 8.535588e-06 2.641523e-03
## DRC3 137.06878 1.0825485 0.2977215 3.636112 2.767843e-04 3.313734e-02
## LRRN3 633.65442 -1.0854341 0.2764544 -3.926268 8.627391e-05 1.572294e-02
## CNTNAP2 4171.45604 0.9935461 0.2676223 3.712494 2.052273e-04 2.736697e-02
## PDE12 480.11478 -1.2114780 0.2024925 -5.982830 2.192939e-09 2.115800e-06
## BNIP3 1246.26202 -1.0472415 0.2984669 -3.508736 4.502414e-04 4.558555e-02
## SOX11 9439.85367 -0.9051936 0.2148164 -4.213801 2.511087e-05 6.184634e-03
## KCTD12 869.92665 -0.8456710 0.2433435 -3.475215 5.104436e-04 4.924880e-02
## H2AW 237.55017 -1.2704323 0.2474902 -5.133263 2.847616e-07 1.459581e-04
## CFAP65 100.52835 1.0091133 0.2464402 4.094759 4.226079e-05 9.002098e-03
## NKX2-5 55.91924 -2.7459226 0.6538525 -4.199605 2.673807e-05 6.355911e-03
## GAS6 527.65113 0.9487736 0.2578042 3.680210 2.330420e-04 2.984389e-02
## PDE4B 1161.27207 -0.7834277 0.2117972 -3.698953 2.164910e-04 2.835340e-02
## ZNF829 136.11596 -1.0374287 0.2569918 -4.036816 5.418143e-05 1.097141e-02
## TPCN1 714.21855 0.6051168 0.1699369 3.560832 3.696813e-04 4.042342e-02
## LINC01551 38.76308 4.6406928 1.2778643 3.631601 2.816689e-04 3.347778e-02
## BCAM 554.21718 0.8381213 0.2368970 3.537915 4.033006e-04 4.240344e-02
## DNAJB13 24.12380 1.8361519 0.5012056 3.663470 2.488212e-04 3.099745e-02
## PCDH18 2951.58289 -0.8586920 0.2236685 -3.839128 1.234720e-04 2.036503e-02
## MYBPC1 121.76197 -2.5123666 0.7005787 -3.586130 3.356213e-04 3.849553e-02
## ZNF471 243.28340 -1.3543080 0.2996731 -4.519285 6.204896e-06 2.120265e-03
## ZNF493 506.98777 -0.5995286 0.1306029 -4.590468 4.422535e-06 1.611965e-03
## ZNF605 961.46814 -0.9817251 0.1317127 -7.453532 9.087419e-14 1.656132e-10
## ZFP28 209.04556 -1.1020145 0.2931105 -3.759723 1.701014e-04 2.423237e-02
## ZNF100 556.84237 -1.4588955 0.1564802 -9.323196 1.128878e-20 3.703170e-17
## CFAP43 213.28265 0.8625323 0.2291546 3.763976 1.672328e-04 2.423237e-02
## ZNF667 174.50297 -1.3977108 0.2371525 -5.893722 3.775915e-09 3.259609e-06
## MT-CYB 45319.46793 0.6870109 0.1414984 4.855257 1.202308e-06 5.189540e-04
## MT-ND2 39999.33168 0.7808431 0.1491730 5.234480 1.654499e-07 9.357618e-05
## MT-ND1 34332.71491 0.7897981 0.1856308 4.254672 2.093556e-05 5.450556e-03
## MT-ATP6 54288.71385 0.7356833 0.1324817 5.553092 2.806598e-08 1.841353e-05
## FANK1 72.93393 1.2667167 0.3298365 3.840438 1.228150e-04 2.036503e-02
## PCDHA4 740.50651 -0.7720398 0.1316070 -5.866254 4.457521e-09 3.655613e-06
## PCDHA2 172.14628 -3.6385853 0.3354445 -10.847057 2.059507e-27 2.814025e-23
## MEG3 5389.42705 -6.8660490 0.9186393 -7.474151 7.770392e-14 1.593125e-10
## MEG9 66.00836 -5.9956704 0.8111506 -7.391562 1.451134e-13 2.163773e-10
## PRR29 103.52019 1.4689771 0.3772792 3.893607 9.876454e-05 1.723336e-02
## MEG8 58.89027 -2.4505888 0.4952216 -4.948469 7.479947e-07 3.407947e-04
## LINC01515 195.86995 -5.0361825 0.4663008 -10.800286 3.431320e-27 2.814025e-23
## MT-ATP8 13072.88599 0.7342644 0.1334619 5.501676 3.761968e-08 2.373223e-05
## SILC1 263.50428 -1.7542583 0.4164477 -4.212433 2.526341e-05 6.184634e-03
## MCIDAS 15.18667 3.7187332 0.8449311 4.401226 1.076408e-05 3.152722e-03
## PCDHA13 47.98728 1.6259670 0.4670627 3.481260 4.990602e-04 4.865408e-02
## TNFRSF6B 22.78767 -3.9356957 1.0288861 -3.825200 1.306657e-04 2.041123e-02
## ZNF585B 278.29547 -1.2186888 0.1733314 -7.030976 2.050933e-12 2.402815e-09
## FZD10-AS1 332.37868 -5.7213380 0.8695262 -6.579834 4.709741e-11 5.149945e-08
## PURPL 103.46331 1.6335988 0.3494943 4.674178 2.951331e-06 1.210193e-03
## LINC02381 54.13587 1.8333424 0.5279725 3.472421 5.157876e-04 4.947338e-02
## PCDHA3 27.07316 -3.1293753 0.7058229 -4.433655 9.264873e-06 2.762954e-03
## BLOC1S5-TXNDC5 19.56246 4.8548809 1.2662889 3.833944 1.261048e-04 2.041123e-02
## TXNIP 9764.81344 -0.9063041 0.2208495 -4.103718 4.065628e-05 8.891257e-03
## ZNF790-AS1 123.79130 -0.9942417 0.2322395 -4.281104 1.859682e-05 5.083751e-03
## MIR924HG 35.75603 -4.8224722 0.8137372 -5.926326 3.097868e-09 2.822846e-06
## LINC02893 57.59384 1.3085359 0.3644242 3.590695 3.297976e-04 3.836412e-02
## LHX1 43.69816 3.8405836 0.8273769 4.641879 3.452545e-06 1.381186e-03
## LHX1-DT 13.31591 3.8961246 1.0909737 3.571236 3.553003e-04 3.991532e-02
## ZNF229 44.84718 -3.3817807 0.8320010 -4.064635 4.810762e-05 9.988115e-03
## BLACAT1 1298.36493 1.2782732 0.2882446 4.434682 9.220814e-06 2.762954e-03
##
## $AR$resAshr
## log2 fold change (MMSE): Genotype AR vs WT
## Wald test p-value: Genotype AR vs WT
## DataFrame with 17781 rows and 5 columns
## baseMean log2FoldChange lfcSE pvalue padj
## <numeric> <numeric> <numeric> <numeric> <numeric>
## TSPAN6 1899.95350 -0.0010493 0.0615334 0.97617617 0.9969430
## TNMD 1.40474 -0.0106537 0.1642036 0.22254342 NA
## DPM1 753.98864 -0.0403886 0.0625618 0.25080293 0.7661892
## SCYL3 324.26243 -0.0221282 0.0671931 0.47876749 0.8878547
## C1orf112 606.44497 -0.1419023 0.1090634 0.00127186 0.0876281
## ... ... ... ... ... ...
## C8orf44 219.88820 0.02259276 0.0723834 0.393687 0.848049
## C8orf44-SGK3 6.72668 0.00151019 0.1155706 0.857683 0.981561
## NPBWR1 3.20140 0.00222092 0.1169012 0.790540 NA
## PDCD6-AHRR 25.30042 -0.00299776 0.1623399 0.620577 0.938008
## LNCDAT 7.67620 -0.01034970 0.1149481 0.355371 0.825025
##
## $AR$DEGsAshr
## baseMean log2FoldChange lfcSE pvalue padj
## NRXN3 125.92310 0.9126397 0.5902348 6.312865e-05 1.247513e-02
## DSG2 537.93484 0.8359665 0.5148227 7.102070e-05 1.354513e-02
## UBE2T 701.97049 -0.9806010 0.1121235 4.697111e-19 1.284034e-15
## ZNF506 590.46712 -1.0261038 0.1415734 7.173113e-14 1.593125e-10
## HSD17B14 169.46894 0.6351254 0.4204949 1.241619e-04 2.036503e-02
## BMP7 1638.74041 0.8779839 0.2125229 1.104683e-06 4.897028e-04
## GPR50 107.23642 1.1785707 0.7233921 3.074789e-05 7.120976e-03
## UNC5B 725.91188 1.0421259 0.3104101 4.155569e-06 1.585108e-03
## FZD10 1452.12492 -5.6911650 0.6131068 3.074433e-21 1.260671e-17
## CLU 2438.39969 0.8695582 0.2018081 7.219434e-07 3.383233e-04
## EGR2 183.81068 -1.0327598 0.5921705 3.771305e-05 8.359047e-03
## P4HA1 1803.85468 -0.8278875 0.2106695 1.687221e-06 7.095845e-04
## SSUH2 70.59441 -2.0000403 0.4445010 7.649401e-09 5.702976e-06
## APOE 335.84670 0.7949383 0.6497645 1.167535e-04 1.982363e-02
## SPINK5 338.95977 0.9377023 0.4450286 3.082486e-05 7.120976e-03
## LMO2 173.60297 1.0346647 0.9890821 7.785024e-05 1.451022e-02
## TFCP2 1320.40127 -0.6806554 0.1057329 5.305196e-11 5.438489e-08
## SPAG8 109.41046 0.9043269 0.2888817 7.247021e-06 2.330699e-03
## SLC15A4 124.41296 -3.9706744 0.3958319 4.665860e-24 2.550981e-20
## HDC 57.64489 0.6861777 1.1958326 2.703965e-04 3.273311e-02
## CFAP74 57.33016 1.5071054 0.6542686 7.093796e-06 2.327049e-03
## RSPO3 346.42227 0.9886676 0.5156740 3.466762e-05 7.897476e-03
## TRIM4 168.68946 0.9095277 0.7202042 8.173298e-05 1.506275e-02
## VAX1 72.91832 2.9306561 2.0839005 1.987878e-05 5.284352e-03
## LRRC4C 121.95019 0.8265490 0.5696149 8.784400e-05 1.583316e-02
## GLT1D1 35.03359 -5.5941161 1.4423473 4.197058e-07 2.024710e-04
## TMEM132D 168.74525 -8.4980779 1.3078588 2.034921e-13 2.781399e-10
## ANGPT1 55.85853 -2.0493504 0.4839509 2.626337e-08 1.794882e-05
## B3GNT7 38.35613 0.8994310 0.6301310 7.320411e-05 1.380108e-02
## TMSB15B 275.74392 -0.6633349 0.2608410 1.742958e-05 4.845423e-03
## TPPP3 102.76556 0.8831230 0.5675211 6.767717e-05 1.321477e-02
## RSPH1 47.87268 0.6899528 0.7789260 1.910329e-04 2.655357e-02
## PPP1R32 135.35555 0.8181424 0.2442201 5.064903e-06 1.767543e-03
## IFTAP 169.11163 4.1039970 0.5630433 1.077277e-13 1.766949e-10
## CRABP1 12001.80107 -1.0600735 0.3269466 4.835183e-06 1.724058e-03
## ZNF667-AS1 234.54796 -1.3219752 0.2574071 6.319222e-09 4.935614e-06
## ZNF558 27.67133 -4.4452292 1.9417370 4.268358e-06 1.591128e-03
## ZNF439 325.88711 -0.7675315 0.2534955 8.535588e-06 2.641523e-03
## LRRN3 633.65442 -0.7147027 0.4298763 8.627391e-05 1.572294e-02
## PDE12 480.11478 -1.1105677 0.1986193 2.192939e-09 2.115800e-06
## SOX11 9439.85367 -0.7254751 0.3044308 2.511087e-05 6.184634e-03
## H2AW 237.55017 -1.1173641 0.2494239 2.847616e-07 1.459581e-04
## CFAP65 100.52835 0.7539248 0.3633011 4.226079e-05 9.002098e-03
## NKX2-5 55.91924 -1.6501242 1.2052336 2.673807e-05 6.355911e-03
## ZNF829 136.11596 -0.7458310 0.3869659 5.418143e-05 1.097141e-02
## LINC01551 38.76308 0.8205709 1.6643270 2.816689e-04 3.347778e-02
## DNAJB13 24.12380 0.6142944 0.7224778 2.488212e-04 3.099745e-02
## ZNF471 243.28340 -1.0921236 0.3596737 6.204896e-06 2.120265e-03
## ZNF605 961.46814 -0.9425028 0.1297721 9.087419e-14 1.656132e-10
## ZFP28 209.04556 -0.6212233 0.4642478 1.701014e-04 2.423237e-02
## ZNF100 556.84237 -1.3952506 0.1573433 1.128878e-20 3.703170e-17
## ZNF667 174.50297 -1.2558979 0.2358341 3.775915e-09 3.259609e-06
## MT-CYB 45319.46793 0.6348461 0.1659696 1.202308e-06 5.189540e-04
## MT-ND2 39999.33168 0.7349800 0.1539092 1.654499e-07 9.357618e-05
## MT-ND1 34332.71491 0.6476628 0.2663892 2.093556e-05 5.450556e-03
## MT-ATP6 54288.71385 0.7023052 0.1338287 2.806598e-08 1.841353e-05
## FANK1 72.93393 0.7230640 0.5158660 1.228150e-04 2.036503e-02
## PCDHA4 740.50651 -0.7391587 0.1305034 4.457521e-09 3.655613e-06
## PCDHA2 172.14628 -3.6022444 0.3347542 2.059507e-27 2.814025e-23
## MEG3 5389.42705 -6.4386068 0.9011922 7.770392e-14 1.593125e-10
## MEG9 66.00836 -5.6885513 0.7948997 1.451134e-13 2.163773e-10
## PRR29 103.52019 0.8096358 0.5873932 9.876454e-05 1.723336e-02
## MEG8 58.89027 -2.0978304 0.6513969 7.479947e-07 3.407947e-04
## LINC01515 195.86995 -4.9453502 0.4625909 3.431320e-27 2.814025e-23
## MT-ATP8 13072.88599 0.7001340 0.1353783 3.761968e-08 2.373223e-05
## SILC1 263.50428 -1.1546873 0.6259759 2.526341e-05 6.184634e-03
## MCIDAS 15.18667 2.7491262 1.5254740 1.076408e-05 3.152722e-03
## TNFRSF6B 22.78767 -1.2092311 1.7232238 1.306657e-04 2.041123e-02
## ZNF585B 278.29547 -1.1431862 0.1709485 2.050933e-12 2.402815e-09
## FZD10-AS1 332.37868 -5.3834598 0.8492106 4.709741e-11 5.149945e-08
## PURPL 103.46331 1.3073952 0.4144333 2.951331e-06 1.210193e-03
## PCDHA3 27.07316 -2.3426023 1.2403810 9.264873e-06 2.762954e-03
## BLOC1S5-TXNDC5 19.56246 1.3727224 2.0578874 1.261048e-04 2.041123e-02
## TXNIP 9764.81344 -0.6922104 0.3288879 4.065628e-05 8.891257e-03
## ZNF790-AS1 123.79130 -0.8053930 0.3135949 1.859682e-05 5.083751e-03
## MIR924HG 35.75603 -4.5591386 0.8042174 3.097868e-09 2.822846e-06
## LHX1 43.69816 3.2488715 1.2653518 3.452545e-06 1.381186e-03
## LHX1-DT 13.31591 0.6569610 1.3712051 3.553003e-04 3.991532e-02
## ZNF229 44.84718 -1.6924821 1.5933962 4.810762e-05 9.988115e-03
## BLACAT1 1298.36493 1.0242981 0.3576873 9.220814e-06 2.762954e-03DEA for Day50
DEAList_day50_HT <- readRDS(paste0(params$InputFolder, 'day50/Output/Savings/day50CbO.DEAList_HT.rds'))
DEAList_day50_AR <- readRDS(paste0(params$InputFolder, 'day50/Output/Savings/day50CbO.DEAList_AR.rds'))
DEAList_day50_HT
## $dds
## class: DESeqDataSet
## dim: 17673 14
## metadata(1): version
## assays(4): counts mu H cooks
## rownames(17673): TSPAN6 TNMD ... NPBWR1 PDCD6-AHRR
## rowData names(47): Gene EnsGene ... deviance maxCooks
## colnames(14): OLE_010 OLE_011 ... OLE_048 OLE_049
## colData names(12): SampleNumber SampleID_GU ... lib.size sizeFactor
##
## $HT
## $HT$res
## log2 fold change (MLE): Genotype HT vs WT
## Wald test p-value: Genotype HT vs WT
## DataFrame with 17673 rows and 6 columns
## baseMean log2FoldChange lfcSE stat pvalue padj
## <numeric> <numeric> <numeric> <numeric> <numeric> <numeric>
## TSPAN6 1022.69733 -0.113571 0.1088076 -1.04377 0.296589803 0.46422519
## TNMD 7.74747 2.675421 0.9693185 2.76011 0.005778269 0.02123805
## DPM1 566.77011 -0.122239 0.0911219 -1.34149 0.179763013 0.32447589
## SCYL3 326.10166 -0.120111 0.0949914 -1.26444 0.206072526 0.35935167
## C1orf112 220.67316 -0.487005 0.1295828 -3.75825 0.000171104 0.00106128
## ... ... ... ... ... ... ...
## LINC01949 6.08511 -0.533526 0.608744 -0.876439 0.380792 0.553295
## C8orf44 175.25242 -0.221174 0.171898 -1.286660 0.198213 0.348982
## C8orf44-SGK3 11.64862 -0.974339 0.604945 -1.610624 0.107262 0.221581
## NPBWR1 3.66410 1.095843 1.038395 1.055324 0.291277 0.458602
## PDCD6-AHRR 40.02742 1.661350 2.417512 0.687215 0.491947 0.657452
##
## $HT$DEGs
## baseMean log2FoldChange lfcSE stat pvalue padj
## TNMD 7.747472 2.6754212 0.96931846 2.760106 5.778269e-03 2.123805e-02
## STPG1 65.812213 -0.6235108 0.21717451 -2.871013 4.091587e-03 1.599170e-02
## HS3ST1 14.255409 3.0124979 0.81654757 3.689311 2.248622e-04 1.341895e-03
## HECW1 487.012064 0.8998175 0.14022555 6.416930 1.390502e-10 3.824984e-09
## TMEM176A 25.491782 -2.0059545 0.72412383 -2.770182 5.602504e-03 2.071062e-02
## KLHL13 805.517717 0.8119393 0.14104425 5.756628 8.581068e-09 1.547450e-07
## CYP26B1 2066.779889 1.3435384 0.35285664 3.807604 1.403197e-04 8.936937e-04
## PDK4 24.639527 -1.9826830 0.55612120 -3.565200 3.635795e-04 2.038624e-03
## SLC25A13 685.642382 -0.9047285 0.13729488 -6.589674 4.407920e-11 1.337815e-09
## SKAP2 64.500162 1.7490964 0.32458828 5.388662 7.098432e-08 1.020878e-06
## MCUB 78.457896 -1.2395485 0.33726890 -3.675253 2.376140e-04 1.406360e-03
## PRKAR2B 2149.632951 0.7112178 0.09503448 7.483786 7.221125e-14 3.409867e-12
## GCFC2 139.052502 0.6269703 0.23428556 2.676094 7.448566e-03 2.628460e-02
## CROT 195.452210 -0.6264758 0.14956193 -4.188739 2.805093e-05 2.166322e-04
## SOX8 440.265741 1.6229314 0.26294019 6.172246 6.732680e-10 1.591778e-08
## ITGA3 260.507308 0.6724120 0.16871128 3.985578 6.731607e-05 4.702086e-04
## ITGA2B 134.019740 0.9688376 0.18851132 5.139413 2.755975e-07 3.492227e-06
## CRLF1 18.764256 3.6201803 0.63811239 5.673264 1.401018e-08 2.378025e-07
## CACNG3 49.962057 1.8704266 0.57996491 3.225069 1.259425e-03 5.851430e-03
## TMEM132A 3655.584391 0.7894159 0.12498370 6.316151 2.681579e-10 6.905165e-09
## TAC1 182.897862 -0.7656924 0.31097869 -2.462202 1.380869e-02 4.389298e-02
## CACNA1G 772.587817 1.0883896 0.23693178 4.593683 4.354898e-06 4.119562e-05
## ALDH3B1 57.244239 1.0738323 0.41529878 2.585686 9.718541e-03 3.280528e-02
## SCIN 13.585603 1.8413892 0.67269777 2.737320 6.194198e-03 2.255157e-02
## DNAH9 22.899935 3.2366585 0.67390785 4.802821 1.564461e-06 1.666386e-05
## GAS7 281.832223 0.9759929 0.24954658 3.911065 9.188997e-05 6.172299e-04
## TKTL1 293.479618 1.8058084 0.18469186 9.777412 1.407639e-22 1.793705e-20
## PAX6 1451.617069 -0.6093800 0.18362219 -3.318662 9.044985e-04 4.432964e-03
## BAIAP3 1063.001823 0.7271966 0.12300230 5.912057 3.378614e-09 6.768946e-08
## E2F2 269.826168 -1.1122790 0.23616769 -4.709700 2.480815e-06 2.520078e-05
## SYN1 721.454609 0.6161452 0.10768182 5.721906 1.053358e-08 1.851957e-07
## CAMK1G 114.341248 0.6594771 0.22834891 2.888024 3.876707e-03 1.531070e-02
## NFIX 115.808109 3.5142409 0.72407042 4.853452 1.213308e-06 1.325765e-05
## ST3GAL1 135.727967 1.2456746 0.14923637 8.346991 7.002403e-17 5.098809e-15
## TENM1 1133.760447 0.9120483 0.14270628 6.391087 1.647102e-10 4.398194e-09
## MLXIPL 59.548735 0.5988461 0.23820486 2.513996 1.193718e-02 3.903570e-02
## CD9 193.882636 2.1480194 0.34470316 6.231505 4.619761e-10 1.124445e-08
## NCAPD2 2723.707691 -0.5870980 0.09841789 -5.965358 2.440977e-09 5.115130e-08
## LRRC23 227.418610 0.7976638 0.20306072 3.928204 8.558276e-05 5.795816e-04
## SYT7 965.302871 0.6732342 0.20154729 3.340329 8.367922e-04 4.143317e-03
## ANLN 559.936125 -1.0618559 0.21650067 -4.904631 9.360299e-07 1.041837e-05
## BRCA1 621.295024 -1.0916569 0.20568637 -5.307386 1.112087e-07 1.533211e-06
## EHD3 342.978006 0.6221504 0.10472630 5.940728 2.837596e-09 5.847270e-08
## MAMLD1 291.210473 0.7119429 0.12528880 5.682414 1.328066e-08 2.269762e-07
## TACC3 1159.637511 -0.9861690 0.14372034 -6.861722 6.803551e-12 2.386752e-10
## MTMR11 113.993913 0.8724068 0.20788453 4.196593 2.709597e-05 2.100059e-04
## STMN4 4436.952174 0.7085134 0.11733632 6.038313 1.557335e-09 3.411961e-08
## ATP1A2 2625.086059 2.1834367 0.28790891 7.583776 3.356399e-14 1.661897e-12
## ZNF582 118.445905 -0.9380685 0.15324260 -6.121461 9.272147e-10 2.122673e-08
## SYT13 1975.687935 0.6686761 0.13805416 4.843578 1.275218e-06 1.387290e-05
## CD74 15.453855 -1.5049913 0.51523903 -2.920958 3.489574e-03 1.398197e-02
## ADGRA2 66.488811 0.9601402 0.35853911 2.677923 7.408022e-03 2.616888e-02
## PLEKHB1 34.543679 1.0912017 0.37321336 2.923801 3.457855e-03 1.388430e-02
## CPS1 590.870863 -1.7230416 0.24826487 -6.940336 3.911689e-12 1.418192e-10
## GRAMD1B 587.202951 1.2164202 0.16141581 7.535942 4.848213e-14 2.346914e-12
## DEPDC1 307.825618 -1.0787636 0.23424472 -4.605284 4.119025e-06 3.917821e-05
## TYMP 19.180540 -1.4559062 0.45598309 -3.192895 1.408540e-03 6.462801e-03
## FAS 113.681992 -1.6531942 0.25540643 -6.472798 9.620457e-11 2.719780e-09
## VRK2 38.370869 -2.9150557 0.51744529 -5.633553 1.765338e-08 2.941665e-07
## TNFRSF1B 20.531579 -1.8261562 0.55502612 -3.290217 1.001103e-03 4.816521e-03
## ARHGAP31 82.086978 0.8215074 0.24312055 3.379013 7.274668e-04 3.678728e-03
## LRRC7 771.709600 0.6573541 0.16399449 4.008391 6.113373e-05 4.326041e-04
## TMSB10 12568.018286 0.6901659 0.05933620 11.631448 2.852187e-31 7.061199e-29
## DEPDC1B 351.717126 -0.9176015 0.19189528 -4.781783 1.737476e-06 1.833767e-05
## FLT4 137.237414 -0.6587485 0.20226701 -3.256826 1.126654e-03 5.337593e-03
## TNC 555.584575 2.1903828 0.45409344 4.823639 1.409625e-06 1.515512e-05
## DSG2 401.819038 -2.1621773 0.18610932 -11.617781 3.347188e-31 8.169969e-29
## PREX2 591.448627 -1.0993578 0.17898198 -6.142282 8.134447e-10 1.887148e-08
## ANO2 35.165313 -1.3376513 0.33088684 -4.042625 5.285616e-05 3.797667e-04
## COL9A2 112.687942 0.8091058 0.20368525 3.972334 7.117196e-05 4.927727e-04
## NEDD4L 3733.242616 0.8386599 0.06638800 12.632704 1.394039e-36 4.930347e-34
## RAD51 101.135116 -1.3701430 0.30302240 -4.521590 6.137692e-06 5.586460e-05
## POLQ 248.635228 -1.2305640 0.23194767 -5.305352 1.124560e-07 1.547944e-06
## MSMO1 7891.326281 0.6416935 0.11605302 5.529313 3.214872e-08 5.011065e-07
## NRIP2 10.076169 1.4961962 0.49587145 3.017307 2.550317e-03 1.072482e-02
## ENTPD2 25.312397 2.4646037 0.65198089 3.780178 1.567164e-04 9.865220e-04
## OPN3 158.297689 -0.6030563 0.20047344 -3.008160 2.628344e-03 1.098895e-02
## HHAT 167.638967 -0.7232529 0.18880865 -3.830613 1.278244e-04 8.241060e-04
## FOXC1 23.672777 2.1787810 0.59751912 3.646379 2.659619e-04 1.552415e-03
## GYG2 165.837279 -0.7645464 0.28836148 -2.651347 8.017142e-03 2.801150e-02
## F7 21.969485 2.1523640 0.49449327 4.352666 1.344920e-05 1.123252e-04
## RASGRF1 94.140182 1.4443405 0.33663671 4.290502 1.782696e-05 1.444325e-04
## CAMK2B 626.022451 0.6163167 0.17732267 3.475679 5.095617e-04 2.720488e-03
## PARP12 24.405251 -1.6764611 0.35854180 -4.675776 2.928443e-06 2.914986e-05
## YBX3 1001.227899 -0.6815838 0.12168804 -5.601075 2.130269e-08 3.486077e-07
## RIMBP2 473.676494 0.8109779 0.11555218 7.018283 2.246110e-12 8.517523e-11
## MPC1 425.661915 0.8267666 0.19554097 4.228099 2.356739e-05 1.859849e-04
## PRDM6 61.628043 -0.8184650 0.29984987 -2.729583 6.341452e-03 2.300071e-02
## GUCY1B1 398.428899 1.1423971 0.15469321 7.384921 1.525441e-13 6.829161e-12
## SEZ6 591.699557 1.0348366 0.17364541 5.959481 2.530397e-09 5.283347e-08
## NGFR 1703.309930 1.4665600 0.17306752 8.473918 2.372745e-17 1.795619e-15
## EYA2 77.523749 -0.7847873 0.31087927 -2.524412 1.158921e-02 3.805247e-02
## CNN2 1201.727345 -0.7700051 0.16427528 -4.687285 2.768533e-06 2.781373e-05
## ABCA7 347.950748 0.6593548 0.11433941 5.766645 8.086490e-09 1.465888e-07
## HMG20B 779.189544 -1.1079623 0.16652830 -6.653298 2.865977e-11 9.014045e-10
## MCM10 400.286506 -1.3658449 0.28604522 -4.774927 1.797728e-06 1.890451e-05
## ANKRD44 460.609498 0.9615212 0.13226569 7.269619 3.605022e-13 1.531251e-11
## PACC1 356.175655 0.5991247 0.11733555 5.106080 3.289105e-07 4.124471e-06
## TLE2 35.801382 1.1639920 0.39781885 2.925935 3.434229e-03 1.380222e-02
## ME1 9.541013 -3.0033114 0.69635702 -4.312890 1.611341e-05 1.317195e-04
## NGEF 71.459698 1.6592032 0.27583453 6.015212 1.796516e-09 3.891702e-08
## ASPM 1362.616996 -1.3929710 0.23659795 -5.887503 3.920750e-09 7.765325e-08
## FGFR2 1275.552836 -0.9072640 0.14481665 -6.264915 3.730293e-10 9.301222e-09
## KIF26A 285.174118 1.4354425 0.28827657 4.979394 6.378378e-07 7.388856e-06
## PFKP 1032.139835 -0.6702403 0.14146084 -4.737992 2.158461e-06 2.229210e-05
## PHKA1 185.421052 -1.0811016 0.13716143 -7.881965 3.222728e-15 1.932522e-13
## PRKCZ 372.260418 1.0077724 0.17584646 5.730979 9.985254e-09 1.770716e-07
## ATP2B3 174.188111 1.2811794 0.19071394 6.717807 1.844796e-11 6.054983e-10
## COASY 885.297873 0.6382370 0.13156212 4.851222 1.227033e-06 1.338231e-05
## ACSL4 1428.621028 0.7213031 0.05076057 14.209910 7.952779e-46 4.752471e-43
## PRR11 1159.566332 -0.8051860 0.16711847 -4.818055 1.449642e-06 1.553636e-05
## REEP1 1338.125830 0.7891907 0.10385109 7.599253 2.978449e-14 1.504855e-12
## RORA 1277.590519 0.8789024 0.16588804 5.298166 1.169714e-07 1.603729e-06
## TGFBR3 108.485202 -1.0688853 0.38320278 -2.789346 5.281455e-03 1.975558e-02
## PTPN3 284.712207 0.5976931 0.13018953 4.590946 4.412415e-06 4.165330e-05
## FGF10 28.238833 -2.8635967 0.90353457 -3.169327 1.527923e-03 6.900937e-03
## CHAT 23.974671 1.5100323 0.41142935 3.670211 2.423508e-04 1.427095e-03
## NCK2 1093.838024 0.5868832 0.08729080 6.723312 1.776400e-11 5.863812e-10
## TRIP13 237.668862 -1.1084049 0.20326797 -5.452924 4.954816e-08 7.408710e-07
## SPEG 1382.546481 0.7726248 0.11783072 6.557074 5.487380e-11 1.633957e-09
## LNX1 111.678560 1.2856622 0.34964425 3.677058 2.359393e-04 1.399325e-03
## HMMR 371.538865 -0.7340296 0.17332471 -4.234997 2.285548e-05 1.807784e-04
## TRNT1 314.267168 -0.8151645 0.14322767 -5.691390 1.260094e-08 2.170719e-07
## EVC 303.514220 -0.8403210 0.18859958 -4.455582 8.366581e-06 7.341410e-05
## NDE1 552.722825 -0.7507275 0.16175192 -4.641228 3.463455e-06 3.372005e-05
## IRAG1 95.810082 -1.0323551 0.19381558 -5.326481 1.001336e-07 1.397981e-06
## MCM2 1870.272466 -1.0721492 0.15101591 -7.099578 1.251388e-12 4.996903e-11
## GSDMB 606.090468 0.6123023 0.09543013 6.416236 1.396845e-10 3.836342e-09
## ST6GAL1 379.864278 1.4405371 0.25147092 5.728444 1.013559e-08 1.794175e-07
## GLI2 1511.655055 -0.6610411 0.08016228 -8.246286 1.633928e-16 1.146396e-14
## PPP2R2C 289.889331 1.3513444 0.21595847 6.257427 3.913802e-10 9.648108e-09
## TEAD2 1219.154415 -0.7036819 0.12731676 -5.527017 3.257218e-08 5.067108e-07
## CA12 508.558506 1.2588252 0.22212320 5.667239 1.451172e-08 2.455870e-07
## ENO1 10554.040630 -0.7894907 0.10384467 -7.602611 2.902145e-14 1.474903e-12
## SEMA3A 548.021439 -1.5861311 0.15857805 -10.002211 1.490321e-23 2.002114e-21
## GTSE1 486.670135 -1.2186529 0.16964689 -7.183468 6.796513e-13 2.817789e-11
## ZNF37A 110.743181 4.2526613 0.34021059 12.500085 7.457127e-36 2.485231e-33
## CACNG5 225.061635 0.9417253 0.24602984 3.827687 1.293530e-04 8.324127e-04
## WDR62 333.109321 -0.9516515 0.15304493 -6.218118 5.031529e-10 1.212746e-08
## ARHGAP15 22.274407 1.3577565 0.40287511 3.370167 7.512258e-04 3.787087e-03
## PAX2 324.551902 1.9790411 0.45169648 4.381352 1.179454e-05 1.000976e-04
## FMO4 35.197717 -0.7851708 0.28304461 -2.774018 5.536866e-03 2.053807e-02
## RGS11 120.008733 -1.3569287 0.31337098 -4.330103 1.490395e-05 1.231691e-04
## SPAG5 898.227860 -0.6791081 0.12065460 -5.628530 1.817515e-08 3.022796e-07
## TPD52 307.232828 -1.5397031 0.17665671 -8.715792 2.887332e-18 2.338199e-16
## ACACB 238.611693 -0.7798707 0.16863483 -4.624612 3.752997e-06 3.609292e-05
## MCAM 551.118702 0.6415512 0.15742417 4.075303 4.595442e-05 3.363134e-04
## GPC4 2569.023914 -0.6330591 0.15807664 -4.004761 6.208026e-05 4.387646e-04
## MBNL3 331.883748 -0.8409148 0.17297075 -4.861602 1.164398e-06 1.276345e-05
## STXBP2 91.913518 0.6911857 0.18179306 3.802047 1.435058e-04 9.119747e-04
## NAALAD2 669.783603 -0.5982613 0.21106014 -2.834554 4.588975e-03 1.755949e-02
## SLC25A43 46.151083 -1.1898470 0.29051633 -4.095629 4.210240e-05 3.106150e-04
## NEBL 525.999884 0.7665189 0.13769530 5.566777 2.594948e-08 4.140925e-07
## ADCY2 433.464629 0.9056368 0.18779281 4.822532 1.417476e-06 1.522930e-05
## RBFOX1 50.519246 4.4797115 0.64294145 6.967526 3.225621e-12 1.191898e-10
## SLC1A3 2053.191508 0.8388029 0.31104409 2.696733 7.002335e-03 2.494870e-02
## LXN 7.299635 -1.8929005 0.77761417 -2.434241 1.492304e-02 4.681946e-02
## FDFT1 14390.391928 0.6333230 0.12897079 4.910593 9.080144e-07 1.013258e-05
## OPHN1 718.035736 0.8931493 0.09058243 9.860072 6.200465e-23 8.202600e-21
## EPB41L2 901.360735 -0.9322259 0.13060172 -7.137930 9.474693e-13 3.845350e-11
## EPHA6 69.840411 -0.9409610 0.36607072 -2.570435 1.015709e-02 3.404686e-02
## SLC4A4 182.442551 1.4920638 0.17395112 8.577489 9.696656e-18 7.569507e-16
## SESN1 883.220023 -0.8406157 0.08535653 -9.848289 6.972073e-23 9.084664e-21
## CHRNA3 507.218051 -0.7168320 0.26588050 -2.696068 7.016325e-03 2.499340e-02
## KCNN2 59.370934 0.7196554 0.26186449 2.748198 5.992388e-03 2.193665e-02
## NDC80 394.130899 -1.1402453 0.23019798 -4.953325 7.295614e-07 8.323435e-06
## [ reached 'max' / getOption("max.print") -- omitted 2036 rows ]
##
## $HT$resAshr
## log2 fold change (MMSE): Genotype HT vs WT
## Wald test p-value: Genotype HT vs WT
## DataFrame with 17673 rows and 5 columns
## baseMean log2FoldChange lfcSE pvalue padj
## <numeric> <numeric> <numeric> <numeric> <numeric>
## TSPAN6 1022.69733 -0.0835855 0.0948219 0.296589803 0.46422519
## TNMD 7.74747 0.6594355 0.8028949 0.005778269 0.02123805
## DPM1 566.77011 -0.0970572 0.0825753 0.179763013 0.32447589
## SCYL3 326.10166 -0.0938139 0.0853611 0.206072526 0.35935167
## C1orf112 220.67316 -0.4070108 0.1358880 0.000171104 0.00106128
## ... ... ... ... ... ...
## LINC01949 6.08511 -0.109027 0.296977 0.380792 0.553295
## C8orf44 175.25242 -0.130464 0.139202 0.198213 0.348982
## C8orf44-SGK3 11.64862 -0.244396 0.379235 0.107262 0.221581
## NPBWR1 3.66410 0.124427 0.383416 0.291277 0.458602
## PDCD6-AHRR 40.02742 0.051861 0.441572 0.491947 0.657452
##
## $HT$DEGsAshr
## baseMean log2FoldChange lfcSE pvalue padj
## TNMD 7.747472 0.6594355 0.80289494 5.778269e-03 2.123805e-02
## HS3ST1 14.255409 1.5775906 1.04692569 2.248622e-04 1.341895e-03
## HECW1 487.012064 0.8577632 0.14219908 1.390502e-10 3.824984e-09
## TMEM176A 25.491782 -0.6954230 0.66416959 5.602504e-03 2.071062e-02
## KLHL13 805.517717 0.7645500 0.14674769 8.581068e-09 1.547450e-07
## CYP26B1 2066.779889 1.0236067 0.37810526 1.403197e-04 8.936937e-04
## PDK4 24.639527 -1.1884434 0.61408332 3.635795e-04 2.038624e-03
## SLC25A13 685.642382 -0.8647643 0.13886573 4.407920e-11 1.337815e-09
## SKAP2 64.500162 1.4927186 0.32411353 7.098432e-08 1.020878e-06
## MCUB 78.457896 -0.9387770 0.36807050 2.376140e-04 1.406360e-03
## PRKAR2B 2149.632951 0.6881279 0.09786769 7.221125e-14 3.409867e-12
## SOX8 440.265741 1.4525329 0.26028651 6.732680e-10 1.591778e-08
## ITGA2B 134.019740 0.8883232 0.19395976 2.755975e-07 3.492227e-06
## CRLF1 18.764256 3.2687180 0.74943605 1.401018e-08 2.378025e-07
## CACNG3 49.962057 0.9744220 0.62360788 1.259425e-03 5.851430e-03
## TMEM132A 3655.584391 0.7526071 0.12917353 2.681579e-10 6.905165e-09
## CACNA1G 772.587817 0.9568484 0.24483854 4.354898e-06 4.119562e-05
## SCIN 13.585603 0.6783636 0.62486638 6.194198e-03 2.255157e-02
## DNAH9 22.899935 2.5908544 0.86599458 1.564461e-06 1.666386e-05
## GAS7 281.832223 0.8087028 0.27447284 9.188997e-05 6.172299e-04
## TKTL1 293.479618 1.7205352 0.18640894 1.407639e-22 1.793705e-20
## BAIAP3 1063.001823 0.6865672 0.12913628 3.378614e-09 6.768946e-08
## E2F2 269.826168 -0.9831442 0.24174948 2.480815e-06 2.520078e-05
## NFIX 115.808109 2.8887576 0.93975799 1.213308e-06 1.325765e-05
## ST3GAL1 135.727967 1.1939812 0.14743035 7.002403e-17 5.098809e-15
## TENM1 1133.760447 0.8686156 0.14449447 1.647102e-10 4.398194e-09
## CD9 193.882636 1.8810596 0.36461599 4.619761e-10 1.124445e-08
## LRRC23 227.418610 0.6714735 0.22650427 8.558276e-05 5.795816e-04
## ANLN 559.936125 -0.9549735 0.22131150 9.360299e-07 1.041837e-05
## BRCA1 621.295024 -0.9974702 0.20673560 1.112087e-07 1.533211e-06
## MAMLD1 291.210473 0.6677541 0.13234844 1.328066e-08 2.269762e-07
## TACC3 1159.637511 -0.9428606 0.14361740 6.803551e-12 2.386752e-10
## MTMR11 113.993913 0.7550547 0.22737914 2.709597e-05 2.100059e-04
## STMN4 4436.952174 0.6704508 0.12313029 1.557335e-09 3.411961e-08
## ATP1A2 2625.086059 2.0042894 0.30365187 3.356399e-14 1.661897e-12
## ZNF582 118.445905 -0.8876987 0.15508834 9.272147e-10 2.122673e-08
## SYT13 1975.687935 0.6058266 0.14903464 1.275218e-06 1.387290e-05
## CD74 15.453855 -0.7604955 0.53808237 3.489574e-03 1.398197e-02
## PLEKHB1 34.543679 0.6644009 0.40962244 3.457855e-03 1.388430e-02
## CPS1 590.870863 -1.5694256 0.24846764 3.911689e-12 1.418192e-10
## GRAMD1B 587.202951 1.1570221 0.15919869 4.848213e-14 2.346914e-12
## DEPDC1 307.825618 -0.9502479 0.24225063 4.119025e-06 3.917821e-05
## TYMP 19.180540 -0.8756475 0.49787983 1.408540e-03 6.462801e-03
## FAS 113.681992 -1.4914442 0.25370530 9.620457e-11 2.719780e-09
## VRK2 38.370869 -2.5228336 0.61279819 1.765338e-08 2.941665e-07
## TNFRSF1B 20.531579 -1.0042605 0.60188594 1.001103e-03 4.816521e-03
## ARHGAP31 82.086978 0.6269348 0.27543921 7.274668e-04 3.678728e-03
## TMSB10 12568.018286 0.6814710 0.06005098 2.852187e-31 7.061199e-29
## DEPDC1B 351.717126 -0.8290529 0.20208592 1.737476e-06 1.833767e-05
## TNC 555.584575 1.7224760 0.48778992 1.409625e-06 1.515512e-05
## DSG2 401.819038 -2.0897213 0.19127313 3.347188e-31 8.169969e-29
## PREX2 591.448627 -1.0295104 0.17768259 8.134447e-10 1.887148e-08
## ANO2 35.165313 -1.0652944 0.34692296 5.285616e-05 3.797667e-04
## COL9A2 112.687942 0.6846407 0.22666046 7.117196e-05 4.927727e-04
## NEDD4L 3733.242616 0.8299438 0.06650525 1.394039e-36 4.930347e-34
## RAD51 101.135116 -1.1506359 0.30577942 6.137692e-06 5.586460e-05
## POLQ 248.635228 -1.1077426 0.22994263 1.124560e-07 1.547944e-06
## MSMO1 7891.326281 0.5969924 0.12319651 3.214872e-08 5.011065e-07
## NRIP2 10.076169 0.8057117 0.52863101 2.550317e-03 1.072482e-02
## ENTPD2 25.312397 1.4643931 0.76832909 1.567164e-04 9.865220e-04
## HHAT 167.638967 -0.6021321 0.21091334 1.278244e-04 8.241060e-04
## FOXC1 23.672777 1.2884944 0.67317463 2.659619e-04 1.552415e-03
## F7 21.969485 1.5808522 0.53641763 1.344920e-05 1.123252e-04
## RASGRF1 94.140182 1.1681283 0.34399089 1.782696e-05 1.444325e-04
## PARP12 24.405251 -1.3648215 0.35994683 2.928443e-06 2.914986e-05
## YBX3 1001.227899 -0.6368817 0.12900294 2.130269e-08 3.486077e-07
## RIMBP2 473.676494 0.7814320 0.11799355 2.246110e-12 8.517523e-11
## MPC1 425.661915 0.7190435 0.21460239 2.356739e-05 1.859849e-04
## GUCY1B1 398.428899 1.0895907 0.15283239 1.525441e-13 6.829161e-12
## SEZ6 591.699557 0.9697650 0.17382167 2.530397e-09 5.283347e-08
## NGFR 1703.309930 1.3920001 0.17148193 2.372745e-17 1.795619e-15
## CNN2 1201.727345 -0.6939337 0.17762841 2.768533e-06 2.781373e-05
## ABCA7 347.950748 0.6183102 0.12087493 8.086490e-09 1.465888e-07
## HMG20B 779.189544 -1.0475951 0.16485359 2.865977e-11 9.014045e-10
## MCM10 400.286506 -1.1723274 0.28525996 1.797728e-06 1.890451e-05
## ANKRD44 460.609498 0.9252421 0.13225634 3.605022e-13 1.531251e-11
## TLE2 35.801382 0.6889568 0.43359801 3.434229e-03 1.380222e-02
## ME1 9.541013 -2.1157138 0.90317261 1.611341e-05 1.317195e-04
## NGEF 71.459698 1.4719380 0.27358914 1.796516e-09 3.891702e-08
## ASPM 1362.616996 -1.2601162 0.23219468 3.920750e-09 7.765325e-08
## FGFR2 1275.552836 -0.8622177 0.14696533 3.730293e-10 9.301222e-09
## KIF26A 285.174118 1.2377460 0.28510932 6.378378e-07 7.388856e-06
## PFKP 1032.139835 -0.6038054 0.15316524 2.158461e-06 2.229210e-05
## PHKA1 185.421052 -1.0406805 0.13589704 3.222728e-15 1.932522e-13
## PRKCZ 372.260418 0.9406259 0.17722155 9.985254e-09 1.770716e-07
## ATP2B3 174.188111 1.1967660 0.18754791 1.844796e-11 6.054983e-10
## ACSL4 1428.621028 0.7155171 0.05108957 7.952779e-46 4.752471e-43
## PRR11 1159.566332 -0.7313288 0.17902751 1.449642e-06 1.553636e-05
## REEP1 1338.125830 0.7652595 0.10584032 2.978449e-14 1.504855e-12
## RORA 1277.590519 0.8147867 0.17258425 1.169714e-07 1.603729e-06
## TGFBR3 108.485202 -0.6136344 0.41197675 5.281455e-03 1.975558e-02
## FGF10 28.238833 -1.0035408 0.95709257 1.527923e-03 6.900937e-03
## CHAT 23.974671 1.0684179 0.44400161 2.423508e-04 1.427095e-03
## TRIP13 237.668862 -1.0167318 0.20326750 4.954816e-08 7.408710e-07
## SPEG 1382.546481 0.7395804 0.12166303 5.487380e-11 1.633957e-09
## LNX1 111.678560 0.9637983 0.38031289 2.359393e-04 1.399325e-03
## HMMR 371.538865 -0.6390869 0.19108101 2.285548e-05 1.807784e-04
## TRNT1 314.267168 -0.7662216 0.14915573 1.260094e-08 2.170719e-07
## EVC 303.514220 -0.7450745 0.20430053 8.366581e-06 7.341410e-05
## NDE1 552.722825 -0.6743899 0.17548916 3.463455e-06 3.372005e-05
## IRAG1 95.810082 -0.9490872 0.19629746 1.001336e-07 1.397981e-06
## MCM2 1870.272466 -1.0232583 0.14972587 1.251388e-12 4.996903e-11
## ST6GAL1 379.864278 1.2892918 0.24686907 1.013559e-08 1.794175e-07
## GLI2 1511.655055 -0.6428594 0.08236856 1.633928e-16 1.146396e-14
## PPP2R2C 289.889331 1.2412984 0.21203318 3.913802e-10 9.648108e-09
## TEAD2 1219.154415 -0.6567162 0.13503388 3.257218e-08 5.067108e-07
## CA12 508.558506 1.1457841 0.21885865 1.451172e-08 2.455870e-07
## ENO1 10554.040630 -0.7655744 0.10582692 2.902145e-14 1.474903e-12
## SEMA3A 548.021439 -1.5219813 0.15819185 1.490321e-23 2.002114e-21
## GTSE1 486.670135 -1.1531416 0.16718324 6.796513e-13 2.817789e-11
## ZNF37A 110.743181 4.2026150 0.34319091 7.457127e-36 2.485231e-33
## CACNG5 225.061635 0.7734686 0.27311184 1.293530e-04 8.324127e-04
## WDR62 333.109321 -0.9017119 0.15439254 5.031529e-10 1.212746e-08
## ARHGAP15 22.274407 0.9105352 0.44408139 7.512258e-04 3.787087e-03
## PAX2 324.551902 1.4902226 0.47508362 1.179454e-05 1.000976e-04
## RGS11 120.008733 -1.1194503 0.32041405 1.490395e-05 1.231691e-04
## SPAG5 898.227860 -0.6350088 0.12784573 1.817515e-08 3.022796e-07
## TPD52 307.232828 -1.4609820 0.17557562 2.887332e-18 2.338199e-16
## ACACB 238.611693 -0.7001358 0.18261454 3.752997e-06 3.609292e-05
## MBNL3 331.883748 -0.7653085 0.18396819 1.164398e-06 1.276345e-05
## SLC25A43 46.151083 -0.9808211 0.30692688 4.210240e-05 3.106150e-04
## NEBL 525.999884 0.7176653 0.14492411 2.594948e-08 4.140925e-07
## ADCY2 433.464629 0.8206519 0.19782965 1.417476e-06 1.522930e-05
## RBFOX1 50.519246 4.2956286 0.67134124 3.225621e-12 1.191898e-10
## OPHN1 718.035736 0.8767450 0.09062942 6.200465e-23 8.202600e-21
## EPB41L2 901.360735 -0.8968172 0.13108224 9.474693e-13 3.845350e-11
## SLC4A4 182.442551 1.4163259 0.17253701 9.696656e-18 7.569507e-16
## SESN1 883.220023 -0.8258933 0.08573464 6.972073e-23 9.084664e-21
## NDC80 394.130899 -1.0195247 0.23237775 7.295614e-07 8.323435e-06
## TCF7 111.696159 -1.5635780 0.29654406 1.819091e-09 3.925883e-08
## ARG2 345.081013 0.6256698 0.13064076 4.406662e-08 6.646428e-07
## STK17B 177.081242 -0.8554177 0.21759756 3.552769e-06 3.448852e-05
## ZNF506 962.327475 0.6208659 0.11363297 1.199390e-09 2.688930e-08
## PCDHA6 296.195905 3.1209433 0.31997928 4.736670e-25 7.015939e-23
## PGR 24.032531 -0.9350518 0.85663109 1.912697e-03 8.364128e-03
## SERTAD4 795.485996 1.4532558 0.16116771 6.861592e-21 7.721519e-19
## TRAF5 101.415939 -1.1842021 0.34680897 1.626345e-05 1.327582e-04
## LYRM2 1028.536379 -0.8809687 0.07483407 9.925374e-33 2.606163e-30
## PLOD1 242.133783 -0.6875288 0.31529300 8.629754e-04 4.254726e-03
## ZNF671 140.840542 -1.1010592 0.21290580 2.128301e-08 3.486077e-07
## SLCO1A2 139.594979 3.1285375 0.31103471 2.412175e-26 3.800273e-24
## EFR3B 1751.877875 0.5903274 0.18872692 5.102135e-05 3.682633e-04
## KIF3C 4319.863302 0.6023546 0.06947780 1.002189e-19 1.027689e-17
## MECOM 89.985242 3.6050725 0.40896597 1.582692e-20 1.735953e-18
## OVGP1 136.008284 0.9456670 0.15573359 1.467956e-10 4.010581e-09
## ORC1 210.576080 -1.1833541 0.22265559 8.929921e-09 1.605348e-07
## RAD54L 234.230732 -1.2337034 0.21035925 3.783097e-10 9.365867e-09
## MAST2 3220.188799 0.7029323 0.10129350 1.521944e-13 6.829161e-12
## EPDR1 241.452195 0.9000096 0.15627529 7.931098e-10 1.844912e-08
## HBQ1 6.559051 -0.9851499 0.80377562 1.520114e-03 6.872836e-03
## PPEF1 57.691395 0.8091799 0.34782309 4.996582e-04 2.674206e-03
## TRIP6 275.792394 -1.1209387 0.17854886 4.265707e-11 1.299204e-09
## BAX 799.257173 -0.7162476 0.06843482 6.279169e-27 1.066843e-24
## ADAMTS2 135.102911 1.3855640 0.42866141 1.383202e-05 1.151893e-04
## MT3 79.628533 0.7051887 0.49305587 4.251150e-03 1.646274e-02
## GNAO1 4552.249667 0.5927987 0.05740865 1.189671e-26 1.926822e-24
## AURKA 300.278380 -0.9914771 0.22506292 6.713440e-07 7.738474e-06
## GP6 22.577373 0.6142667 0.34124814 2.627868e-03 1.098895e-02
## TPX2 1709.906575 -1.0349423 0.16511888 4.935188e-11 1.479702e-09
## SLC4A11 29.522371 -1.4208622 0.41166451 6.621182e-06 5.957689e-05
## CPXM1 1732.311448 -0.9311296 0.08372028 2.027233e-29 4.504095e-27
## TESC 38.528571 -0.8706273 0.33769762 2.449484e-04 1.440433e-03
## BIRC5 867.249319 -1.1606635 0.23089062 3.914320e-08 5.966154e-07
## IRAK3 34.463668 -0.7316807 0.28647724 2.949696e-04 1.705078e-03
## KIF4A 730.454231 -1.0681275 0.23605548 4.122533e-07 4.985589e-06
## PUS7 248.025204 -0.6865120 0.15679592 3.595553e-07 4.434941e-06
## LAMB1 414.330555 0.6843124 0.58031455 5.930887e-03 2.174072e-02
## ABCC6 7.352935 -0.5991774 0.55461332 9.527558e-03 3.224855e-02
## NLRP1 13.796473 0.7291549 0.53659557 4.219445e-03 1.638352e-02
## ZFHX4 2940.527602 -1.0053600 0.17435033 9.402161e-10 2.149597e-08
## RGS17 575.541394 0.5938164 0.09093100 1.567694e-12 6.132763e-11
## MYH7 148.921807 1.4693108 0.33617218 2.186238e-07 2.833769e-06
## SEMA6A 2382.053881 0.7387983 0.13034934 6.195240e-10 1.478836e-08
## WDR76 170.177471 -1.9418282 0.23753813 3.106147e-19 2.957666e-17
## COL9A3 53.562081 0.9695474 0.48890090 7.158719e-04 3.630688e-03
## CLSPN 398.813772 -0.7428961 0.22160887 2.400967e-05 1.890448e-04
## CDC45 183.122205 -1.1630991 0.29699942 3.609933e-06 3.498460e-05
## COMT 334.310116 -6.2678284 0.34471921 9.823899e-75 1.891646e-71
## ADA2 157.297438 -0.7408660 0.22566980 3.040100e-05 2.325019e-04
## XYLB 50.307399 -1.0409517 0.29834040 1.689706e-05 1.375416e-04
## CDC6 264.023284 -1.0963213 0.28045003 4.127490e-06 3.921568e-05
## EPB41L4B 226.844879 0.7559146 0.15030206 2.078035e-08 3.419376e-07
## CYP26A1 420.931158 -1.3529330 0.70074047 2.106317e-04 1.269210e-03
## CRTAC1 115.948218 0.6718855 0.34076237 1.516901e-03 6.860098e-03
## FKBP5 652.044694 -0.9495623 0.08646333 9.841034e-29 2.079819e-26
## PCDH11Y 28.507227 0.7360721 0.45255290 2.766723e-03 1.147065e-02
## HNRNPM 4415.756986 -0.6089637 0.09319301 1.563863e-12 6.132763e-11
## SLC7A4 11.454227 -4.6046071 0.88946172 3.161345e-09 6.392779e-08
## SEZ6L 2049.299359 0.9889352 0.29399746 2.567680e-05 2.000804e-04
## LGALS1 71.686130 1.2568887 0.49244825 1.011132e-04 6.698365e-04
## SOX10 12.272518 0.8163050 1.18557450 2.940419e-03 1.206733e-02
## CENPM 118.687481 -0.7672282 0.21567317 1.202597e-05 1.017130e-04
## SEPTIN3 12294.134164 0.6614896 0.08131416 1.261031e-17 9.756102e-16
## SLC5A4 4.345687 0.7348124 0.91266436 4.032553e-03 1.581447e-02
## TIMP3 275.667631 1.0044593 0.42216763 3.033876e-04 1.743850e-03
## MCM5 955.075706 -0.8794455 0.17585069 3.888773e-08 5.932434e-07
## TSPO 49.359249 -1.2938861 0.32372038 1.908296e-06 1.994618e-05
## RASD2 78.213329 0.6901931 0.46245857 4.073060e-03 1.593366e-02
## APOL4 20.507939 1.5797718 0.59197682 2.598091e-05 2.017677e-04
## PNPLA3 322.158923 0.9305688 0.08838558 1.279315e-26 2.052827e-24
## [ reached 'max' / getOption("max.print") -- omitted 1544 rows ]
DEAList_day50_AR
## $dds
## class: DESeqDataSet
## dim: 17673 14
## metadata(1): version
## assays(4): counts mu H cooks
## rownames(17673): TSPAN6 TNMD ... NPBWR1 PDCD6-AHRR
## rowData names(47): Gene EnsGene ... deviance maxCooks
## colnames(14): OLE_010 OLE_011 ... OLE_048 OLE_049
## colData names(12): SampleNumber SampleID_GU ... lib.size sizeFactor
##
## $AR
## $AR$res
## log2 fold change (MLE): Genotype AR vs WT
## Wald test p-value: Genotype AR vs WT
## DataFrame with 17673 rows and 6 columns
## baseMean log2FoldChange lfcSE stat pvalue padj
## <numeric> <numeric> <numeric> <numeric> <numeric> <numeric>
## TSPAN6 1022.69733 0.244252 0.1192471 2.048285 0.0405320 0.1526386
## TNMD 7.74747 0.671671 1.1834179 0.567569 0.5703278 NA
## DPM1 566.77011 0.181490 0.0999239 1.816287 0.0693263 0.2169459
## SCYL3 326.10166 -0.077452 0.1058136 -0.731967 0.4641889 0.6804306
## C1orf112 220.67316 0.333052 0.1356996 2.454331 0.0141147 0.0735165
## ... ... ... ... ... ... ...
## LINC01949 6.08511 -0.435760 0.705506 -0.6176550 0.536803 NA
## C8orf44 175.25242 0.217527 0.189150 1.1500194 0.250136 0.479973
## C8orf44-SGK3 11.64862 -0.676492 0.684428 -0.9884044 0.322955 NA
## NPBWR1 3.66410 -0.603128 1.068740 -0.5643352 0.572526 NA
## PDCD6-AHRR 40.02742 0.259541 2.661601 0.0975133 0.922319 0.962337
##
## $AR$DEGs
## baseMean log2FoldChange lfcSE stat pvalue padj
## HECW1 487.01206 -0.6907292 0.15649437 -4.413764 1.015888e-05 3.214922e-04
## CYP26B1 2066.77989 -1.7743093 0.39521143 -4.489519 7.138414e-06 2.456187e-04
## SLC7A2 71.45486 0.8495051 0.21178343 4.011197 6.041161e-05 1.315440e-03
## PRKAR2B 2149.63295 -0.6062280 0.10519453 -5.762923 8.266931e-09 8.676709e-07
## ITGA3 260.50731 -0.7856492 0.18879742 -4.161334 3.163933e-05 7.890018e-04
## TAC1 182.89786 -1.2284544 0.33653780 -3.650272 2.619630e-04 4.048494e-03
## MAP3K9 1045.22555 -0.5908176 0.09412563 -6.276905 3.453788e-10 5.927920e-08
## SYN1 721.45461 -0.6133381 0.12050585 -5.089696 3.586379e-07 2.051831e-05
## TFAP2B 5409.28759 -0.6033988 0.22197892 -2.718271 6.562415e-03 4.287464e-02
## MGST1 437.04491 0.7509057 0.16476438 4.557452 5.177790e-06 1.897959e-04
## ST3GAL1 135.72797 -0.7938796 0.17708847 -4.482955 7.361645e-06 2.527036e-04
## GABRA3 551.70082 -0.6320979 0.21014021 -3.007982 2.629889e-03 2.244570e-02
## SLC7A14 261.11613 -0.7694304 0.18421051 -4.176908 2.954984e-05 7.484420e-04
## MAMLD1 291.21047 -0.6021508 0.14274938 -4.218237 2.462194e-05 6.507419e-04
## POLA2 314.19462 0.6243013 0.15170496 4.115233 3.867884e-05 9.301450e-04
## CNTN1 1292.52799 -0.8980093 0.18133330 -4.952258 7.335713e-07 3.822168e-05
## SYT13 1975.68793 -0.6820510 0.15259826 -4.469585 7.837133e-06 2.658975e-04
## CPS1 590.87086 0.7858847 0.26918313 2.919517 3.505743e-03 2.758645e-02
## TNFRSF1B 20.53158 1.3483326 0.49969137 2.698331 6.968817e-03 4.468927e-02
## LRRC7 771.70960 -0.7323077 0.18193853 -4.025028 5.696851e-05 1.261174e-03
## FLT4 137.23741 0.5858991 0.20703866 2.829902 4.656229e-03 3.357871e-02
## PTPRN 430.82937 -0.6589206 0.14964135 -4.403332 1.066008e-05 3.344513e-04
## CAMK2B 626.02245 -0.7008505 0.19618301 -3.572432 3.536807e-04 5.134177e-03
## RIMBP2 473.67649 -0.7310915 0.12911898 -5.662153 1.494853e-08 1.425386e-06
## GUCY1B1 398.42890 -0.5971475 0.17760624 -3.362199 7.732440e-04 9.231471e-03
## SEZ6 591.69956 -1.0928209 0.19510850 -5.601093 2.130043e-08 1.930137e-06
## DGKA 131.46923 -0.6339446 0.20161166 -3.144385 1.664365e-03 1.601677e-02
## ANKRD44 460.60950 -0.6781740 0.14879171 -4.557875 5.167383e-06 1.897959e-04
## MPPED2 195.15180 -1.0001391 0.30323302 -3.298252 9.728862e-04 1.091803e-02
## FGFR2 1275.55284 0.8701210 0.15596172 5.579068 2.418108e-08 2.151084e-06
## PRKCZ 372.26042 -0.6296375 0.19742566 -3.189238 1.426483e-03 1.428343e-02
## NAV3 705.74594 -0.9376056 0.15338510 -6.112755 9.792536e-10 1.414488e-07
## ATP2B3 174.18811 -0.7659533 0.22044869 -3.474520 5.117687e-04 6.720246e-03
## REEP1 1338.12583 -0.6745331 0.11535704 -5.847351 4.994627e-09 5.614326e-07
## RORA 1277.59052 -0.6784940 0.18510667 -3.665422 2.469315e-04 3.903016e-03
## SPTB 51.02704 -1.5217026 0.49162931 -3.095224 1.966646e-03 1.807902e-02
## JMJD6 709.60535 -0.6042578 0.10151187 -5.952583 2.639437e-09 3.291175e-07
## WIPI1 273.05663 -0.5901246 0.16842401 -3.503803 4.586639e-04 6.230398e-03
## LNX1 111.67856 -1.3153893 0.41472685 -3.171700 1.515493e-03 1.494897e-02
## TRNT1 314.26717 0.6254685 0.15333473 4.079105 4.520940e-05 1.051954e-03
## PPP2R2C 289.88933 -0.9463518 0.24261314 -3.900662 9.593016e-05 1.890797e-03
## FOSL2 149.84291 -0.9459509 0.28439173 -3.326225 8.803079e-04 1.009655e-02
## ACTL6B 584.34135 -0.5881736 0.15456370 -3.805380 1.415867e-04 2.559613e-03
## RUNX1T1 2142.26638 -0.7259861 0.14760562 -4.918418 8.724667e-07 4.404297e-05
## MID2 74.23563 -0.7168293 0.21487353 -3.336052 8.497725e-04 9.857507e-03
## ZNF506 962.32747 -1.2589937 0.12422565 -10.134733 3.874317e-24 9.420403e-21
## PCDHA6 296.19590 -1.4038942 0.37162810 -3.777686 1.582924e-04 2.776401e-03
## SERTAD4 795.48600 -1.1602950 0.18501410 -6.271387 3.578465e-10 6.070491e-08
## ZNF671 140.84054 -1.3109240 0.24191472 -5.418951 5.994981e-08 4.508288e-06
## SLCO1A2 139.59498 1.0204619 0.34723595 2.938814 3.294706e-03 2.635223e-02
## B4GALT1 105.08576 1.0061745 0.32751762 3.072123 2.125420e-03 1.914059e-02
## TRIP6 275.79239 0.6302696 0.19403048 3.248302 1.160960e-03 1.230904e-02
## PPP1R13B 302.63845 -0.6434349 0.17285260 -3.722449 1.973000e-04 3.312325e-03
## LHX5 1171.05998 -0.7357898 0.24907485 -2.954091 3.135916e-03 2.555859e-02
## PUS7 248.02520 0.5957092 0.15108028 3.942998 8.046941e-05 1.653476e-03
## ITGA6 659.49194 0.6335637 0.19973883 3.171961 1.514136e-03 1.494569e-02
## RAPGEF4 203.96388 -0.7466078 0.26071889 -2.863651 4.187898e-03 3.129982e-02
## MYO15A 173.82548 -0.7563342 0.26970261 -2.804327 5.042179e-03 3.567427e-02
## HAUS4 282.74382 0.6000578 0.12675042 4.734168 2.199552e-06 9.607563e-05
## MYH7 148.92181 -1.5324051 0.39006220 -3.928617 8.543565e-05 1.735962e-03
## TBC1D2 100.36716 -0.9549873 0.20160530 -4.736915 2.169956e-06 9.506755e-05
## SORBS1 1870.38956 -0.8139636 0.11202627 -7.265828 3.707611e-13 1.590892e-10
## FKBP5 652.04469 0.6067950 0.09035786 6.715465 1.874677e-11 4.635535e-09
## SYDE2 74.81199 0.7509018 0.25763322 2.914616 3.561269e-03 2.797811e-02
## GCAT 184.02729 0.6814468 0.15931227 4.277428 1.890648e-05 5.336350e-04
## HMOX1 109.61352 -0.9664701 0.33468844 -2.887671 3.881057e-03 2.967544e-02
## CACNA1I 139.64094 -0.6910552 0.21947057 -3.148738 1.639774e-03 1.583234e-02
## MLC1 333.92944 -1.0562664 0.36730063 -2.875754 4.030632e-03 3.056283e-02
## SLC8A3 173.22246 -0.5883779 0.21684964 -2.713299 6.661702e-03 4.334793e-02
## GINS1 572.76183 0.6298919 0.13355635 4.716301 2.401714e-06 1.041116e-04
## SALL4 979.82904 0.8420850 0.17988104 4.681344 2.850006e-06 1.177868e-04
## EEF1A2 2804.26303 -0.8454354 0.16411694 -5.151420 2.585208e-07 1.558496e-05
## RSPO4 17.10572 -1.7747848 0.60488034 -2.934109 3.345069e-03 2.665276e-02
## PAK5 688.93372 -0.6078029 0.11893983 -5.110171 3.218675e-07 1.893437e-05
## PXMP4 55.47597 -0.8919618 0.28885404 -3.087933 2.015542e-03 1.842402e-02
## SLC32A1 159.37572 -1.0480505 0.39106540 -2.679988 7.362487e-03 4.647829e-02
## MAP1LC3A 316.96118 -0.7841432 0.21015916 -3.731187 1.905796e-04 3.221251e-03
## SYNDIG1 73.38811 -1.5612687 0.37857761 -4.124039 3.722863e-05 9.048500e-04
## CELF4 1137.94217 -1.0377688 0.18142766 -5.720014 1.065151e-08 1.042918e-06
## LAMA1 1523.04638 0.6854075 0.18509644 3.702975 2.130860e-04 3.489014e-03
## NOL4 270.45722 -0.8733645 0.17997077 -4.852813 1.217226e-06 5.860760e-05
## GLRA2 368.11726 -0.5964749 0.19137762 -3.116743 1.828606e-03 1.717807e-02
## PCSK1N 1068.34148 -0.7938771 0.13883006 -5.718337 1.075714e-08 1.046239e-06
## PCYT1B 578.97050 -0.8526841 0.29425309 -2.897792 3.758001e-03 2.902355e-02
## NALCN 160.49898 -0.9790393 0.26363728 -3.713584 2.043443e-04 3.383858e-03
## FGF14 320.14051 -0.7650080 0.20973199 -3.647551 2.647523e-04 4.082950e-03
## HSF4 256.97648 -0.9801072 0.21595324 -4.538516 5.665151e-06 2.055942e-04
## CBLN1 658.76042 -1.1952750 0.28825606 -4.146574 3.374877e-05 8.316906e-04
## NDRG4 5440.45822 -0.6614156 0.09254452 -7.146999 8.869584e-13 3.405220e-10
## SMPD3 831.99622 -0.7035602 0.16113199 -4.366359 1.263346e-05 3.839783e-04
## COTL1 2455.05714 0.6383814 0.22782189 2.802107 5.076997e-03 3.574725e-02
## NDRG1 369.35800 -0.7079784 0.12098240 -5.851912 4.859537e-09 5.538733e-07
## TUBB4A 817.07522 -0.6112838 0.16602248 -3.681934 2.314711e-04 3.710915e-03
## OLFM2 888.35290 -0.6002730 0.10736759 -5.590821 2.259990e-08 2.022760e-06
## ICAM5 372.27628 -0.8596440 0.30318919 -2.835339 4.577715e-03 3.322601e-02
## PLA2G4C 164.03506 -0.8797805 0.27116419 -3.244457 1.176748e-03 1.242302e-02
## PLEKHA4 88.49805 0.6288101 0.22709752 2.768899 5.624609e-03 3.820691e-02
## LSR 69.82980 1.1389656 0.41318387 2.756559 5.841314e-03 3.930869e-02
## ADAP1 277.83758 -0.6935407 0.16197118 -4.281877 1.853232e-05 5.280626e-04
## CHN2 512.35806 -0.5907985 0.18039336 -3.275057 1.056408e-03 1.151864e-02
## TFR2 141.02274 -0.6428842 0.18970638 -3.388838 7.018946e-04 8.568988e-03
## RARRES2 250.59407 1.0333329 0.31438458 3.286843 1.013172e-03 1.117246e-02
## SLC1A1 182.38777 -0.9388668 0.22226444 -4.224098 2.398993e-05 6.398337e-04
## APBA1 1178.47207 -0.6075032 0.09492808 -6.399616 1.557686e-10 2.951309e-08
## UNC5B 745.09403 -0.6358846 0.23677464 -2.685611 7.239732e-03 4.590197e-02
## ACTA2 237.53091 0.5877620 0.19212238 3.059310 2.218473e-03 1.972291e-02
## CPEB3 387.33347 -0.6045211 0.14920835 -4.051524 5.088518e-05 1.156330e-03
## NEURL1 195.67888 -0.6716159 0.20053500 -3.349120 8.106856e-04 9.545676e-03
## EBF3 4287.46260 -0.8817441 0.30468928 -2.893912 3.804742e-03 2.930696e-02
## SLC9A3R1 347.95319 0.6059950 0.11965928 5.064337 4.098232e-07 2.326425e-05
## NEIL3 89.90259 0.6299136 0.23417141 2.689968 7.145889e-03 4.544765e-02
## CRYAB 191.95576 -1.0193845 0.37261733 -2.735741 6.223998e-03 4.116134e-02
## ZBTB16 1475.08472 0.7293083 0.16102729 4.529097 5.923618e-06 2.123333e-04
## JHY 123.49121 -0.6145456 0.17082125 -3.597594 3.211740e-04 4.752137e-03
## TMEM109 150.62458 0.7540878 0.24986145 3.018024 2.544288e-03 2.180882e-02
## MDK 4935.19503 0.6000171 0.18095701 3.315799 9.138147e-04 1.038290e-02
## PTPN5 633.09891 -0.7079480 0.19528763 -3.625155 2.887878e-04 4.383747e-03
## FZD10 575.91129 -4.4934503 0.89616574 -5.014084 5.328670e-07 2.868633e-05
## TIMELESS 1544.91963 0.6101987 0.07638003 7.988982 1.360576e-15 1.167614e-12
## PRDM13 478.64470 -3.0886164 1.10863311 -2.785968 5.336813e-03 3.693490e-02
## GMNN 399.54015 0.6030139 0.14257937 4.229321 2.343979e-05 6.274551e-04
## ARFGEF3 743.06469 -0.7104958 0.15191243 -4.677009 2.910901e-06 1.196257e-04
## VEGFA 3223.50057 -0.5933773 0.13631652 -4.352937 1.343255e-05 4.023973e-04
## LAMA4 227.72897 -1.1394380 0.26700242 -4.267519 1.976586e-05 5.503133e-04
## SEMA5A 452.89603 -0.7963641 0.26979412 -2.951747 3.159814e-03 2.569595e-02
## HBEGF 117.97187 -0.8550975 0.20143364 -4.245058 2.185369e-05 5.926086e-04
## LOX 52.91890 -0.9307586 0.34764299 -2.677340 7.420925e-03 4.680669e-02
## CDH9 71.05775 -1.4707326 0.30217618 -4.867136 1.132271e-06 5.524652e-05
## GABRG2 250.76094 -0.7653228 0.19583931 -3.907912 9.309724e-05 1.847885e-03
## IRX4 109.14909 -1.1547042 0.37554308 -3.074758 2.106732e-03 1.904282e-02
## PDE4D 644.61321 -0.7640558 0.14976739 -5.101617 3.367640e-07 1.957390e-05
## FGF1 61.26147 -2.1461114 0.50910241 -4.215481 2.492467e-05 6.562314e-04
## STC2 377.19120 -1.0170877 0.20226161 -5.028575 4.941382e-07 2.699994e-05
## RBP1 78.17264 0.7070523 0.22585640 3.130539 1.744858e-03 1.661030e-02
## HES1 193.37661 0.6500032 0.21633440 3.004622 2.659107e-03 2.256697e-02
## CBLB 3110.26108 -0.6175992 0.14049973 -4.395732 1.103999e-05 3.434168e-04
## SLC4A3 453.10081 -0.7103553 0.20234735 -3.510574 4.471409e-04 6.113719e-03
## FNDC4 357.63594 -0.6405876 0.11772042 -5.441601 5.280379e-08 4.075950e-06
## REEP6 166.66410 0.6120657 0.19675477 3.110805 1.865782e-03 1.744865e-02
## EFHD1 45.27727 1.0971606 0.40501176 2.708960 6.749449e-03 4.376343e-02
## ABCB6 356.18783 -0.8998530 0.24444336 -3.681233 2.321084e-04 3.713824e-03
## SLC5A7 84.10572 -1.3582683 0.40332656 -3.367664 7.580793e-04 9.074020e-03
## CHD5 880.41216 -1.3151600 0.19128616 -6.875353 6.183639e-12 1.640238e-09
## DNAJC6 1202.22654 -0.5991277 0.12356222 -4.848794 1.242145e-06 5.961070e-05
## PADI2 74.93590 -1.0878750 0.27551545 -3.948508 7.863970e-05 1.625035e-03
## ID3 300.37043 0.9848902 0.35857870 2.746650 6.020733e-03 4.033429e-02
## PLPPR4 144.22961 -0.9718173 0.19916815 -4.879381 1.064193e-06 5.245103e-05
## RCAN3 233.93395 -0.8551895 0.20102898 -4.254061 2.099283e-05 5.764108e-04
## SLC8A2 471.20168 -1.0713419 0.15553857 -6.887950 5.660194e-12 1.529196e-09
## TTR 1756.71399 5.6839770 1.65676324 3.430772 6.018662e-04 7.661978e-03
## CA14 867.00386 0.6588013 0.16292095 4.043687 5.261722e-05 1.190128e-03
## ATP10B 23.79733 -2.6889323 0.97334113 -2.762580 5.734658e-03 3.873284e-02
## SGIP1 1031.61306 -0.6744190 0.11418647 -5.906295 3.498868e-09 4.253749e-07
## PLAGL1 1832.94449 0.7622864 0.18147199 4.200573 2.662402e-05 6.913515e-04
## STBD1 18.53196 -2.0402858 0.67999636 -3.000436 2.695931e-03 2.274890e-02
## NEK6 513.50080 0.6865989 0.19449893 3.530091 4.154169e-04 5.777423e-03
## ACOT2 26.63873 -1.5925513 0.49438887 -3.221252 1.276317e-03 1.314816e-02
## BCL11A 1120.51422 -1.0980020 0.37709399 -2.911746 3.594146e-03 2.816058e-02
## PPP1R3C 202.27271 -1.1546142 0.28552456 -4.043835 5.258395e-05 1.190128e-03
## MSX2 141.71316 0.6903719 0.22636253 3.049851 2.289553e-03 2.019485e-02
## MOB3B 305.75607 0.8888636 0.23948645 3.711540 2.060019e-04 3.406372e-03
## GRIA2 3436.40870 -0.8062087 0.10123242 -7.963938 1.666486e-15 1.350687e-12
## IQSEC3 263.74290 -0.7711870 0.19019957 -4.054620 5.021588e-05 1.143495e-03
## ENOX1 301.86054 -0.5899052 0.18920155 -3.117867 1.821652e-03 1.713481e-02
## DNAJC15 58.88974 -1.3174093 0.41719704 -3.157763 1.589849e-03 1.548352e-02
## MND1 128.94045 0.6792427 0.24825036 2.736120 6.216838e-03 4.116134e-02
## [ reached 'max' / getOption("max.print") -- omitted 486 rows ]
##
## $AR$resAshr
## log2 fold change (MMSE): Genotype AR vs WT
## Wald test p-value: Genotype AR vs WT
## DataFrame with 17673 rows and 5 columns
## baseMean log2FoldChange lfcSE pvalue padj
## <numeric> <numeric> <numeric> <numeric> <numeric>
## TSPAN6 1022.69733 0.1522423 0.1045269 0.0405320 0.1526386
## TNMD 7.74747 0.0200873 0.2068027 0.5703278 NA
## DPM1 566.77011 0.1213324 0.0877772 0.0693263 0.2169459
## SCYL3 326.10166 -0.0463086 0.0833705 0.4641889 0.6804306
## C1orf112 220.67316 0.2043966 0.1244734 0.0141147 0.0735165
## ... ... ... ... ... ...
## LINC01949 6.08511 -0.03111170 0.192102 0.536803 NA
## C8orf44 175.25242 0.08654881 0.127079 0.250136 0.479973
## C8orf44-SGK3 11.64862 -0.05226779 0.199953 0.322955 NA
## NPBWR1 3.66410 -0.02154627 0.204268 0.572526 NA
## PDCD6-AHRR 40.02742 0.00179369 0.221336 0.922319 0.962337
##
## $AR$DEGsAshr
## baseMean log2FoldChange lfcSE pvalue padj
## CYP26B1 2066.77989 -1.0835803 0.46939809 7.138414e-06 2.456187e-04
## SLC7A2 71.45486 0.6023608 0.23960462 6.041161e-05 1.315440e-03
## ITGA3 260.50731 -0.5867822 0.21136483 3.163933e-05 7.890018e-04
## TAC1 182.89786 -0.6306273 0.37608400 2.619630e-04 4.048494e-03
## MGST1 437.04491 0.6030447 0.18088326 5.177790e-06 1.897959e-04
## ST3GAL1 135.72797 -0.6267032 0.19570080 7.361645e-06 2.527036e-04
## CNTN1 1292.52799 -0.7413694 0.19542325 7.335713e-07 3.822168e-05
## RIMBP2 473.67649 -0.6462762 0.13645402 1.494853e-08 1.425386e-06
## SEZ6 591.69956 -0.9281845 0.19947034 2.130043e-08 1.930137e-06
## FGFR2 1275.55284 0.7584071 0.16420290 2.418108e-08 2.151084e-06
## NAV3 705.74594 -0.8356237 0.15787126 9.792536e-10 1.414488e-07
## REEP1 1338.12583 -0.6033967 0.12107832 4.994627e-09 5.614326e-07
## PPP2R2C 289.88933 -0.6284082 0.27646206 9.593016e-05 1.890797e-03
## RUNX1T1 2142.26638 -0.6089667 0.15941071 8.724667e-07 4.404297e-05
## ZNF506 962.32747 -1.1912259 0.12333412 3.874317e-24 9.420403e-21
## PCDHA6 296.19590 -0.6994985 0.41792184 1.582924e-04 2.776401e-03
## SERTAD4 795.48600 -1.0145416 0.18475458 3.578465e-10 6.070491e-08
## ZNF671 140.84054 -1.0568784 0.24584686 5.994981e-08 4.508288e-06
## MYH7 148.92181 -0.7791067 0.44571466 8.543565e-05 1.735962e-03
## TBC1D2 100.36716 -0.7613363 0.21918921 2.169956e-06 9.506755e-05
## SORBS1 1870.38956 -0.7582790 0.11514212 3.707611e-13 1.590892e-10
## SALL4 979.82904 0.6785370 0.19709059 2.850006e-06 1.177868e-04
## EEF1A2 2804.26303 -0.7158294 0.17582676 2.585208e-07 1.558496e-05
## SYNDIG1 73.38811 -0.8721943 0.43678181 3.722863e-05 9.048500e-04
## CELF4 1137.94217 -0.8954958 0.18602107 1.065151e-08 1.042918e-06
## NOL4 270.45722 -0.7155261 0.19525590 1.217226e-06 5.860760e-05
## PCSK1N 1068.34148 -0.7014512 0.14643851 1.075714e-08 1.046239e-06
## NALCN 160.49898 -0.5969406 0.29951384 2.043443e-04 3.383858e-03
## HSF4 256.97648 -0.7541013 0.23776619 5.665151e-06 2.055942e-04
## CBLN1 658.76042 -0.7848100 0.32588859 3.374877e-05 8.316906e-04
## NDRG4 5440.45822 -0.6166119 0.09547001 8.869584e-13 3.405220e-10
## NDRG1 369.35800 -0.6324720 0.12723716 4.859537e-09 5.538733e-07
## SLC1A1 182.38777 -0.6846382 0.25019870 2.398993e-05 6.398337e-04
## ZBTB16 1475.08472 0.5853223 0.17660000 5.923618e-06 2.123333e-04
## FZD10 575.91129 -4.0299392 1.21947054 5.328670e-07 2.868633e-05
## LAMA4 227.72897 -0.7916409 0.29911133 1.976586e-05 5.503133e-04
## HBEGF 117.97187 -0.6395226 0.22596112 2.185369e-05 5.926086e-04
## CDH9 71.05775 -1.0672426 0.32234353 1.132271e-06 5.524652e-05
## PDE4D 644.61321 -0.6491157 0.16098947 3.367640e-07 1.957390e-05
## FGF1 61.26147 -1.0319144 0.68147757 2.492467e-05 6.562314e-04
## STC2 377.19120 -0.8314402 0.21459402 4.941382e-07 2.699994e-05
## CHD5 880.41216 -1.1571236 0.18972621 6.183639e-12 1.640238e-09
## PADI2 74.93590 -0.6944796 0.31423763 7.863970e-05 1.625035e-03
## PLPPR4 144.22961 -0.7868665 0.21425458 1.064193e-06 5.245103e-05
## RCAN3 233.93395 -0.6407654 0.22540970 2.099283e-05 5.764108e-04
## SLC8A2 471.20168 -0.9697724 0.15542084 5.660194e-12 1.529196e-09
## SGIP1 1031.61306 -0.6048738 0.11972067 3.498868e-09 4.253749e-07
## PPP1R3C 202.27271 -0.7429776 0.32463159 5.258395e-05 1.190128e-03
## GRIA2 3436.40870 -0.7612220 0.10351358 1.666486e-15 1.350687e-12
## CSMD2 968.85062 -0.9975840 0.21860932 2.716644e-08 2.373240e-06
## SV2C 181.54089 -0.6870908 0.33478466 1.093457e-04 2.101771e-03
## MYOG 18.32726 -28.4438965 2.73349284 9.108461e-26 2.657667e-22
## OPTN 1270.74730 -0.5907463 0.12929978 3.893876e-08 3.209478e-06
## GRM4 98.25386 -0.6056921 0.24289994 6.270242e-05 1.351205e-03
## MYRF 165.04781 0.6124310 0.26124331 8.791176e-05 1.776378e-03
## BCL11B 272.25764 -0.7782329 0.34983758 4.883559e-05 1.123758e-03
## TUBA4A 47.10089 -0.8856634 0.37207517 2.054090e-05 5.695814e-04
## FOXP2 2111.20008 -1.2294256 0.34846278 2.221390e-07 1.361675e-05
## SH3BP5 1119.36393 -0.7261173 0.11382197 1.333594e-12 4.745318e-10
## LIN28A 354.56596 1.1826473 0.33542393 3.122305e-07 1.844182e-05
## TRIM22 366.51838 -0.5970849 0.13113192 4.083604e-08 3.322214e-06
## SNAP25 1313.11192 -0.5996452 0.13292011 4.904921e-08 3.867994e-06
## ATP8A2 520.75282 -0.6712739 0.26497561 4.259893e-05 1.007254e-03
## GPR12 95.93084 -0.9025200 0.38937905 2.049893e-05 5.695814e-04
## MYH8 44.93433 -28.5494118 4.00270460 3.706420e-13 1.590892e-10
## MYBPH 26.81626 -28.5073035 4.04663738 7.001476e-13 2.760663e-10
## SPINK5 266.61273 1.2096813 0.36170530 4.165138e-07 2.355240e-05
## DUSP26 387.34465 -0.8545376 0.20669771 1.848690e-07 1.162523e-05
## CTIF 3452.04548 -0.5859326 0.06794082 6.605973e-20 9.637454e-17
## BHLHE40 165.75434 -0.9007862 0.28238838 3.425414e-06 1.365392e-04
## TFCP2 940.41623 -0.8827923 0.12649201 4.046111e-14 2.186248e-11
## FAIM2 916.62971 -0.6180551 0.18952595 6.259477e-06 2.211126e-04
## RAPGEF5 578.40470 -0.8124025 0.17901628 3.552327e-08 2.961423e-06
## RALGPS1 1967.56501 -0.5986361 0.08385303 8.719221e-15 5.530640e-12
## PAK6 206.47580 -0.6901740 0.16225023 1.246026e-07 8.225466e-06
## STRA6 231.73094 0.7466667 0.27134291 1.837965e-05 5.251948e-04
## PCDH10 798.86844 -1.5259672 0.28415445 5.095997e-12 1.457755e-09
## RASGEF1B 345.78989 -0.8616650 0.22085778 4.311096e-07 2.425178e-05
## FBN2 2298.65634 0.9271437 0.16349007 1.479995e-10 2.841006e-08
## AMIGO2 87.73563 -0.9021120 0.33424765 1.053664e-05 3.320065e-04
## SLC15A4 112.20080 -5.0520993 0.48001410 1.062696e-26 3.875918e-23
## SYT16 509.77658 -0.8876346 0.12284518 7.231588e-15 4.948901e-12
## FBLN5 392.69902 -0.5983426 0.25039899 8.434588e-05 1.716209e-03
## DISP2 928.92284 -0.6852023 0.15380296 5.194077e-08 4.052213e-06
## CELF6 533.45696 -0.6125166 0.15407709 4.679679e-07 2.566611e-05
## SLC16A3 183.44445 -0.6384142 0.28540993 9.889874e-05 1.931504e-03
## SEMA6C 1542.25573 -0.6840026 0.07433479 2.557235e-22 4.663437e-19
## TMEM108 210.89728 -0.8748787 0.21141470 1.785678e-07 1.132664e-05
## OCIAD2 149.17437 -0.6805368 0.29003243 6.336283e-05 1.355426e-03
## MARCHF1 629.68634 -0.9650702 0.20138525 1.112114e-08 1.074479e-06
## ADM 59.11124 -1.6387235 0.56888963 1.739127e-07 1.112055e-05
## NCAM1 15045.46948 -0.6040832 0.09989683 1.283758e-11 3.229094e-09
## HMGA2 821.36065 1.0684311 0.12470296 1.951475e-19 2.588188e-16
## DLG2 494.01385 -0.8853535 0.13421138 5.325995e-13 2.220027e-10
## MFSD6 246.14968 -0.7333488 0.15721902 1.944913e-08 1.784549e-06
## GLT1D1 21.05085 -5.7269040 1.13401425 1.829680e-08 1.689443e-06
## TMEM132D 29.40525 -6.9913956 1.15043083 5.982587e-11 1.246857e-08
## NRSN1 402.78754 -0.8401904 0.20873777 2.826042e-07 1.682822e-05
## DAB2 53.97830 0.8421024 0.33041481 1.923820e-05 5.397425e-04
## PID1 580.87020 -0.8756672 0.16503355 9.727390e-10 1.414488e-07
## CABYR 94.08751 -0.7397264 0.24448804 9.013170e-06 2.941681e-04
## ANKRD29 176.45918 -0.8484308 0.27057725 4.767036e-06 1.795058e-04
## ROBO3 11317.98063 -0.6337081 0.22892312 2.662751e-05 6.913515e-04
## GPR26 150.22513 -1.0907805 0.31939121 7.595748e-07 3.888223e-05
## ADAMTS1 141.06621 0.6390167 0.41598680 2.674760e-04 4.120599e-03
## PPP2R2B 1211.96384 -0.7428250 0.11576922 1.084261e-12 4.055971e-10
## SLC6A1 752.29630 -0.6983533 0.15808080 6.056844e-08 4.531451e-06
## SYN2 141.47105 -0.8848304 0.21189600 1.531648e-07 9.843704e-06
## LDLRAP1 143.16822 0.6743081 0.17908754 9.057283e-07 4.540780e-05
## NRG2 88.19297 -0.7916451 0.25523028 6.248050e-06 2.211126e-04
## SPTBN4 298.68420 -0.6580827 0.16072756 2.559546e-07 1.555884e-05
## CELF5 2194.90201 -0.6548599 0.11297262 4.981540e-11 1.101147e-08
## ALPL 309.27324 0.7535060 0.24097777 6.473436e-06 2.259353e-04
## B3GALT2 170.10870 -0.5898160 0.26679369 1.345099e-04 2.465282e-03
## INAVA 332.20664 0.7521482 0.13006808 5.536428e-11 1.170593e-08
## EDIL3 757.13929 -0.6231910 0.17082964 1.594858e-06 7.433668e-05
## GPX8 401.52284 0.6172509 0.12604680 7.351421e-09 7.771731e-07
## GRIK2 299.13014 -0.7098055 0.24162197 1.266858e-05 3.842452e-04
## GPR85 366.36805 -0.7125679 0.23547227 9.747524e-06 3.132305e-04
## ADCY1 4192.59841 -0.9742540 0.16570794 4.656809e-11 1.045203e-08
## DIRAS2 491.64407 -1.2545762 0.25280186 9.441800e-10 1.405576e-07
## LRFN5 239.88452 -0.7555097 0.20975036 1.423091e-06 6.697250e-05
## DACT1 702.59990 -0.7116622 0.19975641 1.757110e-06 7.999251e-05
## SCN3B 2362.58124 -0.6462085 0.10394527 3.857663e-12 1.125589e-09
## CYYR1 73.19137 0.9760850 0.22178162 5.484314e-08 4.189040e-06
## IFTAP 149.45787 3.8149250 0.83819006 4.503828e-08 3.590511e-06
## PRTG 3103.66116 0.8499776 0.33579134 1.912060e-05 5.374768e-04
## ZNF667-AS1 190.70671 -1.5692075 0.28796471 2.009081e-12 6.106351e-10
## CACNG2 91.00247 -0.7446820 0.32268174 5.024199e-05 1.143495e-03
## PBX3 5969.08525 -0.7478592 0.18667067 3.253133e-07 1.906023e-05
## ATCAY 3924.16315 -0.6430030 0.07755912 8.689485e-19 1.056424e-15
## HID1 551.38951 -0.5891564 0.11867937 5.817576e-09 6.381400e-07
## LDLRAD4 283.47799 -0.7504070 0.18458666 2.573769e-07 1.558038e-05
## NSG1 2945.24998 -0.6237349 0.15912878 5.645101e-07 3.005707e-05
## FAM110B 388.99118 -0.7000124 0.16057412 7.816056e-08 5.644972e-06
## B3GALNT1 197.27852 -1.2322636 0.28435719 1.589165e-08 1.505475e-06
## KCNAB1 37.03410 -0.6230889 0.39765713 2.999243e-04 4.497016e-03
## PROKR1 100.84072 -0.6275923 0.36503876 2.565635e-04 3.994670e-03
## TMEM266 62.33998 -0.8849505 0.26730724 2.621942e-06 1.115204e-04
## FAM153A 19.36876 -0.7267146 0.60581420 1.287271e-04 2.383248e-03
## NSG2 9145.93140 -0.7988035 0.12241877 6.319986e-13 2.561174e-10
## KSR2 454.26454 -0.6349085 0.14800428 1.180848e-07 7.938890e-06
## CDK5R2 254.97786 -0.6014570 0.19289849 1.057980e-05 3.326482e-04
## DSCAM 208.44759 -0.8230481 0.23509266 1.760066e-06 7.999251e-05
## NEGR1 1444.14733 -0.7479014 0.19680797 7.105949e-07 3.715724e-05
## ABLIM3 450.82719 -0.9006466 0.17580665 2.487179e-09 3.182934e-07
## CHST1 713.47635 -0.6925463 0.25186407 2.249570e-05 6.055162e-04
## CREG2 138.74220 -0.7569511 0.21705381 2.089323e-06 9.208802e-05
## CDK5R1 3338.39565 -0.6056326 0.09483985 1.496095e-12 4.967027e-10
## GRIN1 222.51507 -1.0364348 0.29876100 8.991291e-07 4.523239e-05
## FIBIN 51.00988 -1.0956181 0.38620641 2.685837e-06 1.125968e-04
## NHLH2 732.17858 -1.4226892 0.34224767 5.380537e-09 5.992110e-07
## PCDHB9 184.02553 -0.6974683 0.16436313 1.291169e-07 8.447023e-06
## TMEM151A 113.80417 -0.6928371 0.29070319 5.513640e-05 1.231830e-03
## ZNF154 134.99483 -0.8498836 0.40211347 3.748764e-05 9.084379e-04
## NRXN1 1525.03327 -0.6163013 0.19590145 9.152625e-06 2.973890e-04
## ARHGAP45 528.36201 0.7734520 0.20840832 9.477212e-07 4.718875e-05
## H2AW 274.69296 -0.8976449 0.16669333 6.628125e-10 1.039760e-07
## KCNH8 1733.32830 -0.5934288 0.22802656 4.980784e-05 1.137162e-03
## KCNQ3 412.98841 -1.3393723 0.30165665 3.806476e-09 4.551859e-07
## RALYL 267.28271 -1.2637986 0.42815375 7.571616e-07 3.888223e-05
## SEPTIN5 1728.57986 -0.6958817 0.08509777 2.137494e-18 2.227421e-15
## ANKS1B 1016.40814 -0.8213030 0.26596678 5.921479e-06 2.123333e-04
## PDIA2 329.84095 -0.6198965 0.14449716 1.229487e-07 8.153177e-06
## KCNIP4 65.59152 -0.8022625 0.44207196 6.954168e-05 1.474627e-03
## IKZF1 251.05625 0.6860593 0.14888563 2.580493e-08 2.267880e-06
## ZNF829 93.65336 -1.0039638 0.27083531 5.390929e-07 2.891480e-05
## MYT1L 1171.33178 -0.8328617 0.17439805 1.234753e-08 1.185119e-06
## MAPT 7145.21800 -0.6342886 0.12942554 6.871555e-09 7.371258e-07
## C3orf70 232.29264 -0.6099549 0.24280747 5.863218e-05 1.290173e-03
## VWC2 65.85703 -0.8657934 0.39660172 3.101271e-05 7.787339e-04
## SEMA4A 393.40997 -0.6650841 0.12693169 1.125380e-09 1.578670e-07
## ZNF471 418.29083 -1.2525006 0.27224540 4.635940e-09 5.367756e-07
## ZNF605 821.23079 -0.9315395 0.08671207 1.678997e-28 8.164965e-25
## H2BU1 51.80292 -0.7910088 0.34443311 4.021115e-05 9.632849e-04
## ZNF100 317.72841 -0.8158987 0.13372901 9.759601e-12 2.542550e-09
## COL4A6 431.55589 0.8398355 0.30257889 1.200534e-05 3.678545e-04
## DNM3 783.57924 -0.6756933 0.14743270 2.930906e-08 2.500525e-06
## ZNF667 175.36693 -1.8427466 0.35562436 1.770434e-12 5.614969e-10
## CACNA1E 874.52491 -1.0562702 0.14783576 1.312793e-14 7.980141e-12
## TUSC1 90.27037 -0.9239695 0.35984837 1.201371e-05 3.678545e-04
## LRRTM3 91.32120 -0.6489274 0.42623518 2.478091e-04 3.912648e-03
## PLXNB3 186.04240 -0.8685307 0.30423212 8.850380e-06 2.914124e-04
## ZNF525 143.24205 -0.6845472 0.20877895 4.840865e-06 1.806224e-04
## GP1BB 175.33389 -0.8974986 0.16519123 5.157133e-10 8.267848e-08
## LINC02487 105.40628 -1.5255749 0.81777030 3.609727e-06 1.415653e-04
## PCDHA5 81.91158 -0.7255426 0.23454020 7.708863e-06 2.623469e-04
## PCDHA4 1036.58113 -0.9736976 0.10501985 4.476157e-22 7.255850e-19
## PCDHA2 319.06314 -4.6839904 0.35063185 2.270822e-41 1.656451e-37
## TRIM71 1221.68580 0.7256423 0.29858037 4.276687e-05 1.009589e-03
## XKR4 883.11247 -0.6476978 0.14470422 5.020401e-08 3.937776e-06
## MIR219A2HG 311.47484 0.6971330 0.25104478 2.057505e-05 5.695814e-04
## MEG3 7371.75115 -9.0930050 0.60523993 3.161204e-52 4.611880e-48
## SKOR2 374.49058 -2.6468019 0.81651045 1.302233e-07 8.481376e-06
## GPC1-AS1 53.44658 -0.6426524 0.31171542 1.382371e-04 2.511507e-03
## MEG9 29.44203 -7.0978054 0.96256893 7.462871e-15 4.948901e-12
## LINC02470 47.22127 -7.5383128 1.09173670 2.128254e-13 1.063141e-10
## MEG8 62.24677 -2.2602300 0.49687695 2.029972e-10 3.641494e-08
## LINC01515 75.01665 -3.0635122 0.40975071 5.632265e-15 4.324690e-12
## FEZF1-AS1 31.11261 0.8876431 1.09961696 9.187024e-05 1.833509e-03
## [ reached 'max' / getOption("max.print") -- omitted 16 rows ]Complete DEG List
Already filtered DEGs from DEA
DEA <- list(D0_HT = row.names(DEAList_ips_HT$HT$DEGs),
D0_AR = row.names(DEAList_ips_AR$AR$DEGs),
D25_HT = row.names(DEAList_day25_HT$HT$DEGs),
D25_AR = row.names(DEAList_day25_AR$AR$DEGs),
D50_HT = row.names(DEAList_day50_HT$HT$DEGs),
D50_AR = row.names(DEAList_day50_AR$AR$DEGs))
lapply(DEA, length)
## $D0_HT
## [1] 2574
##
## $D0_AR
## [1] 25
##
## $D25_HT
## [1] 1511
##
## $D25_AR
## [1] 111
##
## $D50_HT
## [1] 2202
##
## $D50_AR
## [1] 652Manual filtering of DEGs
Res <- list(D0_HT = DEAList_ips_HT$HT$res,
D0_AR = DEAList_ips_AR$AR$res,
D25_HT = DEAList_day25_HT$HT$res,
D25_AR = DEAList_day25_AR$AR$res,
D50_HT = DEAList_day50_HT$HT$res,
D50_AR = DEAList_day50_AR$AR$res)
Res <- lapply(Res, as.data.frame)
Res$D0_HT %>% filter(., abs(log2FoldChange) > log2(logFCthr), padj < FDRthr)
Res$D0_AR %>% filter(., abs(log2FoldChange) > log2(logFCthr), padj < FDRthr)
Res$D25_HT %>% filter(., abs(log2FoldChange) > log2(logFCthr), padj < FDRthr)
Res$D25_AR %>% filter(., abs(log2FoldChange) > log2(logFCthr), padj < FDRthr)
Res$D50_HT %>% filter(., abs(log2FoldChange) > log2(logFCthr), padj < FDRthr)
Res$D50_AR %>% filter(., abs(log2FoldChange) > log2(logFCthr), padj < FDRthr)3. Scatterplots
iPSCs
#Extract Results
#NOTE: can extract more top genes using the Num argument, default Num=10
CompareResD0 <- computeCompResFC(Res$D0_HT, Res$D0_AR) ## The number of genes in the first data set is 16981## The number of genes in the second data set is 16616## The number of common genes that will be examined is 16616## Warning in cor.test.default(AllRes$log2FoldChange_A, AllRes$log2FoldChange_B, : Cannot compute
## exact p-value with ties#Extract info on the genes belonging to the four quadrants
quadr <- c('Up_Up', 'Down_Down', 'Up_Down', 'Down_Up')
qDf <- lapply(quadr, {function(q) obj <- CompareResD0$Significant %>%
dplyr::filter(Direction == q & Status == 'SignificantA&B') %>%
dplyr::select(genes, log2FoldChange_A, padj_A,
log2FoldChange_B, padj_B, Log2FcSsum) %>%
arrange(desc(abs(Log2FcSsum)))})
names(qDf) <- quadrCheck DEGs overlap across time-point comparisons
compResFScatter(Res$D0_HT, Res$D0_AR)
## The number of genes in the first data set is 16981
## The number of genes in the second data set is 16616
## The number of common genes that will be examined is 16616
## Warning in cor.test.default(AllRes$log2FoldChange_A, AllRes$log2FoldChange_B, : Cannot compute
## exact p-value with tiesNumber of genes that are:
- Up_Up 0
- Down_Down: 10
- Up_Down: 4
- Down_Up: 1
Concordant Downregulated genes
qDf[['Down_Down']]%>%
DT::datatable(class='hover', rownames=FALSE, escape=TRUE, extension='Buttons',
options=list(dom='Bfrtip', buttons=list(I('colvis'), c('csv', 'excel'))))Discordant Upregulated and Downregulated genes
qDf[['Up_Down']]%>%
DT::datatable(class='hover', rownames=FALSE, escape=TRUE, extension='Buttons',
options=list(dom='Bfrtip', buttons=list(I('colvis'), c('csv', 'excel'))))Discordant Downregulated and Upregulated genes
qDf[['Down_Up']]%>%
DT::datatable(class='hover', rownames=FALSE, escape=TRUE, extension='Buttons',
options=list(dom='Bfrtip', buttons=list(I('colvis'), c('csv', 'excel'))))Day25
#Extract Results
#NOTE: can extract more top genes using the Num argument, default Num=10
CompareResD25 <- computeCompResFC(Res$D25_HT, Res$D25_AR) ## The number of genes in the first data set is 17781## The number of genes in the second data set is 17781## The number of common genes that will be examined is 17781## Warning in cor.test.default(AllRes$log2FoldChange_A, AllRes$log2FoldChange_B, : Cannot compute
## exact p-value with ties#Extract info on the genes belonging to the four quadrants
quadr <- c('Up_Up', 'Down_Down', 'Up_Down', 'Down_Up')
qDf <- lapply(quadr, {function(q) obj <- CompareResD25$Significant %>%
dplyr::filter(Direction == q & Status == 'SignificantA&B') %>%
dplyr::select(genes, log2FoldChange_A, padj_A,
log2FoldChange_B, padj_B, Log2FcSsum) %>%
arrange(desc(abs(Log2FcSsum)))})
names(qDf) <- quadrCheck DEGs overlap across time-point comparisons
compResFScatter(Res$D25_HT, Res$D25_AR)
## The number of genes in the first data set is 17781
## The number of genes in the second data set is 17781
## The number of common genes that will be examined is 17781
## Warning in cor.test.default(AllRes$log2FoldChange_A, AllRes$log2FoldChange_B, : Cannot compute
## exact p-value with tiesNumber of genes that are:
- Up_Up 7
- Down_Down: 9
- Up_Down: 5
- Down_Up: 2
Concordant Upregulated genes
qDf[['Up_Up']]%>%
DT::datatable(class='hover', rownames=FALSE, escape=TRUE, extension='Buttons',
options=list(dom='Bfrtip', buttons=list(I('colvis'), c('csv', 'excel'))))Concordant Downregulated genes
qDf[['Down_Down']]%>%
DT::datatable(class='hover', rownames=FALSE, escape=TRUE, extension='Buttons',
options=list(dom='Bfrtip', buttons=list(I('colvis'), c('csv', 'excel'))))Discordant Upregulated and Downregulated genes
qDf[['Up_Down']]%>%
DT::datatable(class='hover', rownames=FALSE, escape=TRUE, extension='Buttons',
options=list(dom='Bfrtip', buttons=list(I('colvis'), c('csv', 'excel'))))Day50
#Extract Results
#NOTE: can extract more top genes using the Num argument, default Num=10
CompareResD50 <- computeCompResFC(Res$D50_HT, Res$D50_AR) ## The number of genes in the first data set is 17673## The number of genes in the second data set is 17673## The number of common genes that will be examined is 17673## Warning in cor.test.default(AllRes$log2FoldChange_A, AllRes$log2FoldChange_B, : Cannot compute
## exact p-value with ties#Extract info on the genes belonging to the four quadrants
quadr <- c('Up_Up', 'Down_Down', 'Up_Down', 'Down_Up')
qDf <- lapply(quadr, {function(q) obj <- CompareResD50$Significant %>%
dplyr::filter(Direction == q & Status == 'SignificantA&B') %>%
dplyr::select(genes, log2FoldChange_A, padj_A,
log2FoldChange_B, padj_B, Log2FcSsum) %>%
arrange(desc(abs(Log2FcSsum)))})
names(qDf) <- quadrCheck DEGs overlap across time-point comparisons
compResFScatter(Res$D50_HT, Res$D50_AR)
## The number of genes in the first data set is 17673
## The number of genes in the second data set is 17673
## The number of common genes that will be examined is 17673
## Warning in cor.test.default(AllRes$log2FoldChange_A, AllRes$log2FoldChange_B, : Cannot compute
## exact p-value with tiesNumber of genes that are:
- Up_Up 9
- Down_Down: 9
- Up_Down: 49
- Down_Up: 9
Concordant Upregulated genes
qDf[['Up_Up']]%>%
DT::datatable(class='hover', rownames=FALSE, escape=TRUE, extension='Buttons',
options=list(dom='Bfrtip', buttons=list(I('colvis'), c('csv', 'excel'))))Concordant Downregulated genes
qDf[['Down_Down']]%>%
DT::datatable(class='hover', rownames=FALSE, escape=TRUE, extension='Buttons',
options=list(dom='Bfrtip', buttons=list(I('colvis'), c('csv', 'excel'))))Discordant Upregulated and Downregulated genes
qDf[['Up_Down']]%>%
DT::datatable(class='hover', rownames=FALSE, escape=TRUE, extension='Buttons',
options=list(dom='Bfrtip', buttons=list(I('colvis'), c('csv', 'excel'))))Discordant Downregulated and Upregulated genes
qDf[['Down_Up']]%>%
DT::datatable(class='hover', rownames=FALSE, escape=TRUE, extension='Buttons',
options=list(dom='Bfrtip', buttons=list(I('colvis'), c('csv', 'excel'))))Day25 Heterozygous and Day50 Ancestral
#Extract Results
#NOTE: can extract more top genes using the Num argument, default Num=10
CompareResD25ht_50ar <- computeCompResFC(Res$D25_HT, Res$D50_AR) ## The number of genes in the first data set is 17781## The number of genes in the second data set is 17673## The number of common genes that will be examined is 17116## Warning in cor.test.default(AllRes$log2FoldChange_A, AllRes$log2FoldChange_B, : Cannot compute
## exact p-value with ties#Extract info on the genes belonging to the four quadrants
quadr <- c('Up_Up', 'Down_Down', 'Up_Down', 'Down_Up')
qDf <- lapply(quadr, {function(q) obj <- CompareResD25ht_50ar$Significant %>%
dplyr::filter(Direction == q & Status == 'SignificantA&B') %>%
dplyr::select(genes, log2FoldChange_A, padj_A,
log2FoldChange_B, padj_B, Log2FcSsum) %>%
arrange(desc(abs(Log2FcSsum)))})
names(qDf) <- quadrCheck DEGs overlap across time-point comparisons
compResFScatter(Res$D25_HT, Res$D50_AR)
## The number of genes in the first data set is 17781
## The number of genes in the second data set is 17673
## The number of common genes that will be examined is 17116
## Warning in cor.test.default(AllRes$log2FoldChange_A, AllRes$log2FoldChange_B, : Cannot compute
## exact p-value with tiesNumber of genes that are:
- Up_Up 11
- Down_Down: 13
- Up_Down: 23
- Down_Up: 3
Concordant Upregulated genes
qDf[['Up_Up']]%>%
DT::datatable(class='hover', rownames=FALSE, escape=TRUE, extension='Buttons',
options=list(dom='Bfrtip', buttons=list(I('colvis'), c('csv', 'excel'))))Concordant Downregulated genes
qDf[['Down_Down']]%>%
DT::datatable(class='hover', rownames=FALSE, escape=TRUE, extension='Buttons',
options=list(dom='Bfrtip', buttons=list(I('colvis'), c('csv', 'excel'))))Concordant Downregulated genes
qDf[['Up_Down']]%>%
DT::datatable(class='hover', rownames=FALSE, escape=TRUE, extension='Buttons',
options=list(dom='Bfrtip', buttons=list(I('colvis'), c('csv', 'excel'))))4. upsetR
Check DEGs overlap across time-point comparisons.
Heterozygous
upset(fromList(DEA[c(1,3,5)]), order.by = 'freq', nsets=6, matrix.color = 'darkgrey',
keep.order = T, main.bar.color='grey10',
decreasing = T,
mb.ratio = c(0.6, 0.4),
text.scale = 1,
point.size = 3,
line.size = 1)
Ancestral
upset(fromList(DEA[c(2,4,6)]), order.by = 'freq', nsets=6, matrix.color = 'darkgrey',
keep.order = T, main.bar.color='grey10',
decreasing = T,
mb.ratio = c(0.6, 0.4),
text.scale = 1,
point.size = 3,
line.size = 1)
All organoids
upset(fromList(DEA[c(3,4,5,6)]), order.by = 'freq', nsets=6, matrix.color = 'darkgrey',
keep.order = T, main.bar.color='grey10',
decreasing = T,
mb.ratio = c(0.6, 0.4),
text.scale = 1,
point.size = 3,
line.size = 1)
All samples
upset(fromList(DEA), order.by = 'freq', nsets=6, matrix.color = 'darkgrey',
keep.order = T, main.bar.color='grey10',
decreasing = T,
mb.ratio = c(0.6, 0.4),
text.scale = 1,
point.size = 3,
line.size = 1)
5. Venn diagram
venn_plot <- ggvenn(DEA[3:6], show_elements=FALSE, fill_alpha = 0.2, text_size = 4, show_percentage = FALSE, fill_color = c('#FFDAB9', '#80CBC4', '#A0E8A9', '#C8A2C8'))
venn_plot
ggsave(paste0(params$OutputFolder, 'Output/Figures/', 'VennPlotOrganoids_1.pdf'))## Saving 8 x 10 in imagevenn_plot <- ggvenn(DEA[3:6], show_elements=FALSE, fill_alpha = 0.2, text_size = 4, show_percentage = FALSE, fill_color = c('#FFDAB9', '#80CBC4', '#FFDAB9', '#80CBC4' ))
venn_plot
ggsave(paste0(params$OutputFolder, 'Output/Figures/', 'VennPlotOrganoids_2.pdf'))## Saving 8 x 10 in image6. Intersection identities
v.table <- venn(DEA[3:6])
all_intersections <- attr(v.table, "intersections")
for (comparison in names(all_intersections)) {
cat(comparison, "\n")
print(all_intersections[[comparison]])
}
## D25_AR:D50_AR
## [1] "FZD10" "TFCP2" "SLC15A4" "TPPP3" "PFKFB3" "H2AW" "BCAM"
## [8] "ZNF605" "ZNF100" "PCDHA4" "PCDHA13" "FZD10-AS1" "LHX1" "LHX1-DT"
## D25_AR:D50_HT
## [1] "DSG2" "GPR50" "CLU" "LMO2" "GRIA1" "PPP1R32" "SERINC5" "CRABP1"
## D25_HT:D25_AR
## [1] "BMP7" "BMF" "DNAI1" "SSUH2" "MNS1"
## [6] "LEF1" "HDC" "MYBPC1" "BLOC1S5-TXNDC5" "TXNIP"
## D25_HT:D50_AR
## [1] "RUNX1T1" "SORBS1" "EEF1A2" "PCYT1B" "SEMA5A" "CDH9"
## [7] "RBP1" "FNDC4" "BCL11A" "NXPH1" "MMP24" "NOTCH2"
## [13] "STK26" "TNS3" "ARHGAP24" "AMIGO2" "COL2A1" "DISP2"
## [19] "CCDC33" "KIFC3" "GAS8" "CRABP2" "HMGCLL1" "GRM1"
## [25] "ANKRD29" "ROBO3" "ADAMTS1" "VCAM1" "UNCX" "EFNA1"
## [31] "DSCAM" "NEGR1" "SLITRK1" "BACE2" "OAF" "HS6ST3"
## [37] "CPNE4" "LRRTM3" "C2orf72" "ARHGEF35-AS1"
## D25_HT:D50_HT
## [1] "HS3ST1" "KLHL13" "SKAP2" "GCFC2" "CRLF1" "TMEM132A"
## [7] "DNAH9" "GAS7" "TKTL1" "CAMK1G" "NFIX" "TENM1"
## [13] "MTMR11" "ATP1A2" "ZNF582" "CD74" "ADGRA2" "FAS"
## [19] "TMSB10" "COL9A2" "FOXC1" "PARP12" "PRDM6" "NGFR"
## [25] "ME1" "TGFBR3" "FGF10" "NCK2" "SPEG" "ST6GAL1"
## [31] "ZNF37A" "PAX2" "MCAM" "ADCY2" "SESN1" "LYRM2"
## [37] "EFR3B" "PPEF1" "BAX" "ADAMTS2" "GNAO1" "SLC4A11"
## [43] "LAMB1" "WDR76" "COL9A3" "COMT" "CYP26A1" "MFNG"
## [49] "LGALS1" "SOX10" "TIMP3" "RIN3" "DHRS2" "SLCO4A1"
## [55] "RNF125" "TIMP1" "SYTL4" "FGF9" "DGKH" "MAPK3"
## [61] "GDPD3" "TRPA1" "SLC1A6" "TFPI2" "LHX2" "ENG"
## [67] "SH3GL2" "RASSF4" "TLX1" "SFXN3" "PNPO" "SOX6"
## [73] "TNS2" "ELK3" "OAS3" "MDGA1" "KHDRBS2" "ASCC3"
## [79] "PCDHB5" "CDH6" "PDGFRB" "UNC5A" "EHHADH" "MRPL3"
## [85] "POMC" "ITGA4" "HPCAL1" "QPCT" "DLX2" "PRRX1"
## [91] "KIF21B" "ZNHIT6" "SLC2A1" "NENF" "PROX1" "NRP2"
## [97] "RAB32" "ONECUT2" "PYROXD2" "ACAT2" "KIAA1217" "EGR1"
## [103] "TNFRSF10B" "CAT" "ARL4A" "GLIPR2" "PLP1" "CDKN1A"
## [109] "MT2A" "TNFSF9" "CITED1" "FLRT1" "PLEKHG3" "TMEM35A"
## [115] "LRRC61" "GNG11" "RASL11B" "LIF" "DOCK4" "FEZF1"
## [121] "ISLR" "LOXL1" "E2F8" "SOX15" "CD68" "MTUS1"
## [127] "RPS4Y1" "GAMT" "GDPD2" "SH3BP4" "COL5A1" "MED18"
## [133] "HIP1R" "PNCK" "DUSP9" "EDA2R" "RAB11FIP4" "SLC6A6"
## [139] "GFPT2" "SLC6A11" "NUP210" "RAP1GAP2" "BCAN" "PPP1R3D"
## [145] "DCLK1" "POSTN" "STARD13" "NTS" "SWAP70" "RNF122"
## [151] "CAMK1" "SYT6" "CMPK2" "DAGLA" "ADAM19" "BICDL1"
## [157] "MDM2" "SP110" "SERPINE2" "DRAM1" "GPNMB" "GAD2"
## [163] "CTSV" "MYC" "TFAP2A" "FOXF2" "SLCO5A1" "ITGA11"
## [169] "ZNF280D" "IFI44L" "IFI44" "SIX3" "ZNF365" "STAT4"
## [175] "HECW2" "PARP9" "SEMA7A" "HERC5" "CPNE8" "FOXN4"
## [181] "GRTP1" "ARMH4" "NEIL1" "ST8SIA2" "TIGD7" "MAPK4"
## [187] "STAC2" "PLPP2" "PGGHG" "HMCN1" "CGN" "EFNA3"
## [193] "CNGA3" "SLC4A10" "DLX1" "SPAG16" "ITGA9" "IGFBP3"
## [199] "DIAPH2" "RGS20" "STOM" "LCN9" "PROSER2" "PAOX"
## [205] "RGS10" "CDH8" "GPM6A" "FREM2" "TMEM86A" "ABTB3"
## [211] "GFRA1" "TRIM36" "PLEKHH2" "ZNF117" "RASSF3" "NMRAL1"
## [217] "LGI4" "UBASH3B" "PITPNC1" "OBSCN" "DKK2" "PTPRN2"
## [223] "AFF2" "WIF1" "MPV17L" "MMP14" "C2CD2" "PSMG3"
## [229] "XKR8" "CLSTN2" "SLC13A3" "DMTN" "S100B" "LY6E"
## [235] "FDXR" "ZNF75A" "AK4" "NFIA" "DDR2" "SPATA18"
## [241] "TAFA4" "CDS1" "PTX3" "APBB2" "DTX3L" "PRKCD"
## [247] "ARHGEF3" "EXO5" "ERMAP" "ITGA2" "F2RL2" "CMBL"
## [253] "EGFLAM" "UBLCP1" "ACSL6" "DLC1" "SPIDR" "VEGFD"
## [259] "PHOX2A" "PKNOX2" "E2F7" "PACSIN3" "KCNC2" "ADAMTS15"
## [265] "IKBIP" "ALKBH3" "TMEM100" "CHRFAM7A" "ELFN2" "GREM1"
## [271] "TUBA1C" "ZNF528" "PLIN4" "RAB3IL1" "SCARA3" "MMADHC"
## [277] "COL3A1" "GFRA2" "INPP5D" "CHST14" "PCSK9" "KCNK9"
## [283] "ONECUT1" "GPRC5C" "EMB" "SIX2" "DLGAP1" "POLH"
## [289] "PRKCE" "NPTX1" "CLCN5" "DSEL" "ZNF562" "ECEL1"
## [295] "GATM" "CFAP46" "PRNP" "FRMD5" "FRMD3" "ZMAT3"
## [301] "ZNF596" "RARG" "MYD88" "ZNF680" "PARP14" "PTPRM"
## [307] "VEGFB" "TNFRSF10C" "JUP" "HAP1" "CTSF" "MSRB3"
## [313] "PHLDA3" "ZNF25" "ALG10B" "FOSL1" "MTLN" "TUBB6"
## [319] "ZNF135" "HSD11B2" "RIMS2" "RNF152" "BDNF" "BOK"
## [325] "TCERG1L" "TCIM" "KCNA3" "ANXA2R" "ANXA2R-OT1" "ZNF619"
## [331] "ZNF454" "POGLUT3" "NRIP1" "TSPYL5" "ZFP3" "ARSJ"
## [337] "FAM83H" "AEN" "TMEM132E" "TMIE" "ZNF875" "CHST15"
## [343] "KCNIP1" "PLCB1" "RNF32-DT" "SPNS2" "CHST6" "MAGEA2B"
## [349] "CCDC125" "BCOR" "FHL3" "TRIM61" "ZNF703" "ANKRD45"
## [355] "CFAP91" "PNMA3" "ZNF730" "TBX1" "CNTN2" "ALDH1A3"
## [361] "CSF1" "TXNRD2" "LRRC26" "SRY" "TMEM121" "RPS27L"
## [367] "INPP5J" "AHNAK2" "OLFML2A" "NDUFA4L2" "PRAME" "C11orf87"
## [373] "IFIT1" "RTN4RL1" "SHOX" "ZNF225-AS1" "ANKRD37" "ZNF501"
## [379] "HPDL" "PDZD7" "WDR86" "SAMD11" "POTEE" "PRELP"
## [385] "SHISA6" "H1-0" "SP6" "PLAC9" "ZNF527" "ZNF33A"
## [391] "PAX8-AS1" "FAM217B" "ZNF107" "NTNG2" "ARL9" "CACNA1H"
## [397] "AJAP1" "POTEF" "ZNF502" "POTEI" "ARID5A" "ZNF585A"
## [403] "ZNF138" "ZNF429" "ZNF470" "ADARB1" "PDGFA" "EME2"
## [409] "H2BC12" "HES5" "ZNF71" "ZNF560" "ZNF273" "ZNF248"
## [415] "HOXC4" "ZNF583" "ZNF534" "EIF1AY" "INPP5F" "CCDC152"
## [421] "CSAG1" "TCEAL5" "HSPA1A" "HLA-C" "INSYN2B" "PNMA8B"
## [427] "LRRC10B" "MUC19" "C21orf62" "GOLGA8O" "HLA-A" "GPX3"
## [433] "MAGEA12" "ERV3-1" "EMP2" "LTB4R" "FAM66B" "SCRT2"
## [439] "HMX1" "LINC01139" "LINC03010" "CEBPZOS" "LINGO3" "LINC02076"
## [445] "EBF2" "PLXNA4" "ZNF880" "POTEM" "ADM5" "MIR3659HG"
## [451] "LINC01980" "RUSC1-AS1" "LINC01748" "SOX21-AS1" "MIR34AHG" "ZBTB46-AS2"
## [457] "PSMG3-AS1" "TSPAN19" "GOLGA8N" "LNCTAM34A" "HLA-B" "DANT2"
## [463] "GNAS-AS1" "FAM88E" "FOXD2-AS1" "SHISA9" "LINC00649" "PCDHGC3"
## [469] "NECTIN3-AS1" "PDE6B-AS1" "SOX2-OT" "ZNF512" "PTCHD4" "NEAT1"
## [475] "LINC00682" "SLCO5A1-AS1" "MIR4458HG" "CASC9" "LINC02972" "PVT1"
## [481] "GOLGA8K" "AGA-DT" "CHCHD10" "YPEL3-DT" "LINC00491" "LINC02600"
## [487] "LINC02315" "FOXD1" "ZFHX4-AS1" "PCDHGA10" "PCDHGB4" "AP5B1"
## [493] "SALL3" "LINC02306" "DIO3OS" "LINC02301" "LINC02820" "TMEM179"
## [499] "ZNF710-AS1" "PWRN1" "SPON1" "LINC01896" "PARD6G-AS1" "KC6"
## [505] "ZNF285" "MAGEA2" "CSAG3" "MIA-RAB4B" "ZNF470-DT" "LINC01297"
## [511] "TUBGCP5"
## D50_HT:D50_AR
## [1] "PRKAR2B" "ITGA3" "TAC1" "SYT13" "CPS1" "TNFRSF1B" "FLT4"
## [8] "CAMK2B" "SEZ6" "FGFR2" "PRKCZ" "ATP2B3" "REEP1" "RORA"
## [15] "LNX1" "PPP2R2C" "TRIP6" "PUS7" "MYH7" "FKBP5" "CACNA1I"
## [22] "GINS1" "SALL4" "SLC32A1" "MAP1LC3A" "NOL4" "HSF4" "CBLN1"
## [29] "ICAM5" "PLA2G4C" "PLEKHA4" "ADAP1" "CHN2" "TFR2" "RARRES2"
## [36] "EBF3" "NEIL3" "CRYAB" "GMNN" "ARFGEF3" "HBEGF" "GABRG2"
## [43] "HES1" "SLC5A7" "DNAJC6" "PADI2" "CA14" "ATP10B" "IQSEC3"
## [50] "MND1" "SV2C" "GRM4" "PACSIN1" "MIR9-1HG" "OPRL1" "BCL2L12"
## [57] "HIVEP3" "TUBA4A" "CDKN2D" "EGLN3" "CBFA2T3" "GINS2" "LIN28A"
## [64] "TRIM22" "GPR12" "MYBPH" "ALDH1L2" "GABBR2" "ARHGEF39" "PAK6"
## [71] "STRA6" "CYP2C8" "PCDH10" "RASGEF1B" "MTTP" "RTN1" "FBLN5"
## [78] "NOL3" "RHBDL3" "TAF4B" "SLC16A3" "CBLN2" "SUSD4" "ST6GAL2"
## [85] "SCN1A" "CDCA7" "MARCHF4" "VWA5B2" "OCIAD2" "MARCHF1" "SFRP2"
## [92] "PSD2" "EML3" "CNTN5" "LYPD1" "VEGFC" "ADAMTS12" "CCDC3"
## [99] "AKR1C2" "STK32B" "JAKMIP1" "PID1" "CDH12" "GPR26" "CNTNAP5"
## [106] "GOLGA7B" "PPP2R2B" "SLC6A1" "LDLRAP1" "NPM2" "CPAMD8" "GPATCH4"
## [113] "ALPL" "GPX8" "GPR85" "MYORG" "DIRAS2" "LRFN5" "AMER2"
## [120] "RET" "BTNL9" "CDYL2" "PRTG" "YPEL4" "LDLRAD4" "NSG1"
## [127] "FSTL5" "B3GALNT1" "KCNAB1" "PROKR1" "PCDH7" "KCNK3" "KCND3"
## [134] "CDK5R2" "CALB2" "CKS1B" "ABLIM3" "IGDCC3" "DPP10" "CREG2"
## [141] "CDK5R1" "LY6H" "FIBIN" "DSCAML1" "NHLH2" "AURKB" "FAM216B"
## [148] "ARHGAP45" "HHIPL1" "CALN1" "CHEK2" "KCNQ3" "PCDH9" "POU6F1"
## [155] "MAP7D2" "ANKS1B" "GPRIN3" "PARPBP" "SYN3" "DLEU7" "MYT1L"
## [162] "MAPT" "LUZP2" "LIN28B" "DIPK1C" "DNER" "JAKMIP3" "INSYN2A"
## [169] "RASSF10" "PTPRT" "SEMA4A" "SLC6A9" "SLC6A17" "ADGRA1" "DIO3"
## [176] "NUP62CL" "CACNA1E" "HYLS1" "TUSC1" "SMOC1" "PLXNB3" "GRM3"
## [183] "INF2" "LINC02487" "COL15A1" "PCDHA7" "MIR219A2HG" "C2orf74-DT" "SYT3"
## [190] "LCNL1" "SP9" "INHBA-AS1" "LINC02470" "RFPL1S" "LINC01503" "LINC01322"
## [197] "PCP4L1" "EPHA5-AS1" "PCDHGB7" "TMPO-AS1" "LINC01619" "FIGNL2" "GRIN2B"
## [204] "EPOP"
## D25_AR:D50_HT:D50_AR
## [1] "ZNF506" "ZNF671" "UNC5B" "LRRC4C" "GLT1D1" "ZNF585B" "ZNF790-AS1"
## D25_HT:D25_AR:D50_HT
## [1] "CACNA1G" "RSPO3" "VAX1" "ANGPT1" "ZNF558" "LRRN3" "SOX11"
## [8] "PCDH18" "SILC1" "PURPL" "LINC02381" "BLACAT1"
## D25_HT:D50_HT:D50_AR
## [1] "HECW1" "CYP26B1" "SYN1" "ST3GAL1" "MAMLD1" "LRRC7" "RIMBP2"
## [8] "GUCY1B1" "ANKRD44" "TRNT1" "PCDHA6" "SERTAD4" "SLCO1A2" "MLC1"
## [15] "OLFM2" "ACTA2" "PTPN5" "LAMA4" "CHD5" "NEK6" "MSX2"
## [22] "DNAJC15" "CSMD2" "MYRF" "BCL11B" "FOXP2" "NFATC1" "SH3BP5"
## [29] "CTIF" "PI15" "MMRN1" "NTRK3" "CDH11" "CACNA1A" "RBMS3"
## [36] "NKD2" "LHFPL2" "NFIB" "FAM13C" "ADM" "CACNA1C" "DAB2"
## [43] "CA10" "UNC5D" "KIT" "CACNA2D3" "NRG2" "CILP2" "LMX1A"
## [50] "KIF26B" "INHBB" "GUCY1A1" "ZCCHC24" "DACT1" "CYYR1" "RBFOX3"
## [57] "FAM110B" "PLEKHA2" "NSG2" "TNFRSF10D" "UCP2" "GRIN1" "RNF182"
## [64] "COL18A1" "KCNH8" "SEPTIN5" "FAM183A" "C3orf70" "LITAF" "MYT1"
## [71] "TMEM229B" "MMP17" "GP1BB" "NPTXR" "CYP4F26P" "FEZF1-AS1" "ANKRD18B"
## [78] "LINC01122" "MIR210HG" "PCDHA10" "LINC02506" "ZNF528-AS1" "ARHGAP23" "COPG2IT1"
## D25_HT:D25_AR:D50_HT:D50_AR
## [1] "SPINK5" "TRIM4" "TMEM132D" "IFTAP" "ZNF667-AS1" "ZNF439" "ZNF829"
## [8] "ZNF471" "ZNF493" "ZFP28" "ZNF667" "PCDHA2" "MEG3" "MEG9"
## [15] "MEG8" "LINC01515" "PCDHA3" "LINC02893" "ZNF229"
## D25_AR
## [1] "ZMYND10" "NRXN3" "UBE2T" "OSBPL6" "HSD17B14" "PGK1" "RND3"
## [8] "EGR2" "P4HA1" "APOE" "ZFHX2" "SPAG8" "CFAP74" "IGSF1"
## [15] "B3GNT7" "TMSB15B" "RSPH1" "ABHD6" "DRC3" "CNTNAP2" "PDE12"
## [22] "BNIP3" "KCTD12" "CFAP65" "NKX2-5" "GAS6" "PDE4B" "TPCN1"
## [29] "LINC01551" "DNAJB13" "CFAP43" "MT-CYB" "MT-ND2" "MT-ND1" "MT-ATP6"
## [36] "FANK1" "PRR29" "MT-ATP8" "MCIDAS" "TNFRSF6B" "MIR924HG"
## D25_HT
## [1] "CFH" "ENPP4" "SEMA3F" "COPZ2" "TNFRSF12A" "MYLIP"
## [7] "CDKL5" "CELSR3" "MAPK8IP2" "PAX7" "SEMA3G" "CD4"
## [13] "TSPAN9" "PLAUR" "DCN" "CLDN11" "CCDC88C" "BID"
## [19] "WWTR1" "PHLDB1" "MARCO" "SNAI2" "HGF" "RUNX3"
## [25] "SERPINB1" "ABCC2" "ARNTL2" "APBA2" "TLL1" "VCAN"
## [31] "RAI14" "CDH10" "RIPOR3" "USH2A" "ARAP2" "LMO3"
## [37] "ELN" "PPP1R3F" "COL23A1" "HOMER3" "ALX4" "LAMA3"
## [43] "PHPT1" "PLEKHH1" "SLC2A3" "PSD" "COL11A1" "CDH3"
## [49] "TM7SF3" "SNCAIP" "SLC9A3R2" "NTN1" "ERBB3" "ROPN1"
## [55] "PRKCQ" "CTNNA2" "TIE1" "STAG3" "CBFB" "LAPTM4A"
## [61] "ST6GALNAC2" "LMCD1" "CDH19" "SLC6A15" "STK10" "PANX2"
## [67] "PTGS2" "MAP3K13" "SEMA3C" "FSCN1" "SLC46A1" "PAG1"
## [73] "CTTNBP2" "CAPN6" "ITGA8" "SYNJ2" "BRINP1" "FKBP7"
## [79] "TNS1" "MOXD1" "DCT" "COL5A3" "MEF2C" "AACS"
## [85] "OPRK1" "SLC27A5" "FAM234B" "NKAIN1" "COL16A1" "PREP"
## [91] "ABCB1" "WNT11" "MMP2" "SH3BP2" "NID2" "PHACTR3"
## [97] "TFAP2C" "DOCK9" "C3orf18" "ARHGAP28" "SMOX" "FXYD5"
## [103] "PITPNM2" "CCDC80" "CAPN3" "TBX15" "MAP3K1" "PTGS1"
## [109] "MYO3A" "ITPR3" "DSP" "PCSK5" "NRP1" "HCN2"
## [115] "MADCAM1" "P2RX6" "RBFOX2" "IL2RB" "SIX4" "NINL"
## [121] "NFATC2" "CTSZ" "COL20A1" "CHRNA4" "ISM1" "PDYN"
## [127] "PLCB4" "MYL9" "SAMHD1" "MROH8" "SNTA1" "CDH20"
## [133] "ATP11C" "MCF2" "SYP" "ELF4" "ASB9" "KLHL4"
## [139] "GABRE" "RUBCNL" "ACP5" "FLT1" "CRISPLD2" "CRYM"
## [145] "SLC6A2" "LACTB" "AP3B2" "CTSH" "ZDHHC2" "CPQ"
## [151] "CALB1" "SFRP1" "NIPAL2" "PLAT" "GSDMD" "DNASE2"
## [157] "KCNN1" "DLX5" "CPED1" "PTPRZ1" "PCOLCE" "AHR"
## [163] "PRUNE2" "CORO2A" "LHX6" "SHB" "CXCL12" "LIPA"
## [169] "NPM3" "LGI1" "SMARCD2" "CCL2" "PMP22" "CRACD"
## [175] "MAPK10" "INPP4B" "HGFAC" "FAM149A" "SIAE" "CCND1"
## [181] "CEP126" "SLC15A3" "TSPAN11" "WNT5B" "MANSC1" "ARHGDIB"
## [187] "ADGRD1" "ENO2" "COL12A1" "GCNT2" "FAM184A" "SASH1"
## [193] "PHACTR1" "TRIM38" "ADGRG6" "MDFI" "SMOC2" "SLC29A1"
## [199] "GHR" "PCDHB15" "NPR3" "PRLR" "PFKFB4" "C3orf52"
## [205] "ROPN1B" "CISH" "PEX5L" "SPTBN1" "FN1" "KCNJ13"
## [211] "EPHA4" "TNR" "OPRD1" "KCNC4" "DLGAP3" "WLS"
## [217] "OLFML3" "NID1" "HPCAL4" "MFAP2" "CDK18" "FAAH"
## [223] "PLPPR5" "CNR1" "MYB" "FGF23" "KLHL29" "FKBP1B"
## [229] "HOXB8" "HOXB1" "PCDHB10" "TGFBI" "GLT8D2" "TBX2"
## [235] "TMEM131L" "TRIM6" "PDZRN3" "FMOD" "HS3ST2" "TWIST1"
## [241] "CALD1" "ITPR2" "NECAB1" "TNFAIP6" "G0S2" "FAM210B"
## [247] "EDN3" "PTGIS" "PMEPA1" "RUNX2" "SH3TC1" "BMP4"
## [253] "SOX9" "MIF4GD" "EML2" "TMEM74B" "STAT5A" "PRKCG"
## [259] "SIX1" "RHOJ" "CANX" "MASP1" "PLAAT1" "TNFRSF19"
## [265] "ADM2" "PODXL" "LRRC17" "CGNL1" "RNASE1" "STARD8"
## [271] "CNN1" "FAM98C" "UNC13A" "GDF15" "H19" "MNX1"
## [277] "SHFL" "GSE1" "TMEM204" "BARX1" "RARA" "MATN3"
## [283] "TRIM5" "SERPINF1" "DDC" "RIDA" "HSPA12B" "SYT11"
## [289] "KANK4" "BEX2" "BEX1" "ADCK2" "LOXL2" "MEIS2"
## [295] "SPIRE1" "TMEM106C" "RSAD2" "CRB1" "SOX5" "RERG"
## [301] "SPX" "DSC3" "APLNR" "PDGFRA" "ETS1" "TBX3"
## [307] "KCP" "KHDC1" "MRAP2" "ITGA7" "AGAP2" "HEY2"
## [313] "TEC" "SEMA4F" "RAB11FIP5" "NIBAN1" "CHRND" "FLNB"
## [319] "TBC1D4" "PHF11" "LMO7" "BZW2" "ADAMTS7" "SCN7A"
## [325] "NIBAN2" "ANGPTL2" "LMX1B" "ENPP2" "IGFBPL1" "KIAA0319"
## [331] "SLC22A23" "TUBB2A" "CPEB2" "FHDC1" "ARRB1" "SMAD6"
## [337] "GCHFR" "BCAR3" "EMILIN1" "ADAMTS14" "MSTN" "CDK15"
## [343] "APH1B" "CDKL2" "CASP6" "RGS3" "PRICKLE1" "LRIG3"
## [349] "LUM" "ASCL1" "TMEM132B" "FAM222A" "ITGB7" "REM2"
## [355] "FRMD6" "SORD" "TLE3" "DNAJA4" "ARRDC4" "CYP1A1"
## [361] "ADAMTS17" "HAPLN3" "NKD1" "ABCA8" "GNAL" "SLC13A5"
## [367] "TMC6" "TTYH2" "COL6A1" "COL6A2" "ADAMTS10" "SLC6A3"
## [373] "FBN3" "ARHGEF19" "HSPG2" "LMO4" "IGSF3" "ZNF697"
## [379] "RXRG" "ECM1" "CTSK" "KCNH1" "OSR1" "SFXN5"
## [385] "GPR17" "ZNF385B" "UNC80" "OSBPL10" "CTDSPL" "STAC"
## [391] "COL8A1" "NXPE3" "STXBP5L" "ATP10D" "SNCA" "MYO10"
## [397] "PLK2" "HAPLN1" "PAM" "MEGF10" "ARHGAP26" "GABRB2"
## [403] "GFRA3" "DAAM2" "LRP12" "CDKN2B" "AOPEP" "ADAM12"
## [409] "ZNF215" "PAMR1" "KLHL35" "TENM4" "HTR3B" "SCN2B"
## [415] "KIAA1755" "CLEC1A" "PPP1R1C" "C2orf50" "ITPR1" "GPR158"
## [421] "THRB" "NPAS3" "PTPRO" "EDNRA" "FLI1" "TLCD4"
## [427] "PTPN14" "TMEM163" "TCF7L1" "GUCY1A2" "IGSF10" "GJA1"
## [433] "DYNLT5" "PRDM8" "BCL2L11" "RBMS1" "SCN3A" "CNKSR3"
## [439] "AK5" "CHST9" "PRKCA" "LRRK1" "ABCA5" "C4orf19"
## [445] "PDE1C" "PLCL2" "PPM1J" "TTN" "MMP16" "ART3"
## [451] "TSPAN7" "FGF18" "ZIC3" "LHFPL4" "ARSL" "FAM81A"
## [457] "PWWP3B" "AFAP1L1" "SNX22" "COLEC12" "RNF207" "SHROOM4"
## [463] "H2BC5" "CD1C" "NBL1" "ADAMTS4" "MPZ" "TNNI1"
## [469] "RUNX1" "SIM2" "SPON2" "ZDHHC12" "CHRNB2" "PTH1R"
## [475] "AZGP1" "COL26A1" "TAMALIN" "ADCY9" "SHANK2" "LRP5"
## [481] "FBLIM1" "MXRA8" "ADGRL4" "LHX8" "BRINP3" "SLC9C2"
## [487] "PKDCC" "TRIM17" "FRZB" "ACTG2" "EN1" "MSX1"
## [493] "C1QTNF7" "NPPC" "PBXIP1" "FSTL1" "IGFBP7" "FEV"
## [499] "IFI16" "PRICKLE2" "TIPARP" "GYG1" "GRIK3" "CAMK2N2"
## [505] "HEYL" "BDH2" "SPRY1" "HSPA4L" "GRM2" "DUSP7"
## [511] "PITX2" "ADGRV1" "F2RL1" "SHROOM1" "TMEM200A" "SLC29A4"
## [517] "COL1A2" "SLC13A4" "NOS3" "FREM1" "NIPSNAP3B" "C9orf64"
## [523] "CRYL1" "VSTM4" "FRMD7" "NDRG2" "C10orf82" "ARHGAP42"
## [529] "AMOTL1" "GABRB3" "PCBD1" "CLMP" "PPFIBP2" "WDR72"
## [535] "GALR1" "ZCCHC18" "STAT6" "SAMD14" "PRRX2" "IGF2"
## [541] "CACNB3" "TTYH1" "CDC42EP5" "TMEM145" "DNAAF3" "KIFC2"
## [547] "ANGPTL4" "SOST" "CASKIN1" "ABCA3" "MAP4K2" "VASN"
## [553] "FILIP1L" "TAP1" "HR" "BMP1" "GDNF" "SLC16A4"
## [559] "ABHD15" "ATOH8" "SLC35G2" "STXBP6" "PXDC1" "ROR2"
## [565] "AFAP1L2" "SH3TC2" "BNC1" "TACR3" "ROBO1" "IFFO2"
## [571] "MYRIP" "NIPA1" "SP7" "SGCD" "CAVIN4" "GPR27"
## [577] "CYTL1" "HAS2" "S1PR1" "CDC42BPG" "TMEM37" "ZNF561"
## [583] "PLEKHG5" "VAT1L" "LRRC34" "COL8A2" "PWWP2B" "MLLT3"
## [589] "AQP4" "SCG2" "SYNPO" "SERF1A" "ISG20" "STARD5"
## [595] "IL16" "SYNPO2" "CES3" "MIR4435-2HG" "GXYLT2" "BNC2"
## [601] "SLC2A14" "INSM1" "PPP1R14B" "CSPG4" "ADGRG2" "WFIKKN2"
## [607] "GPR160" "SPTBN2" "C1QTNF1" "CMKLR1" "CD248" "SEZ6L2"
## [613] "CTBP2" "PHYHD1" "PCSK1" "DENND2C" "FOXG1" "ZSCAN2"
## [619] "PLAAT3" "PHLDB3" "NCKAP5" "SCN4B" "RIMKLA" "FZD8"
## [625] "LINC02904" "HIC1" "ZNF491" "NECTIN3" "ZNF354C" "MAMDC4"
## [631] "PARD6G" "P4HTM" "CA8" "ERFE" "RFLNA" "CDH4"
## [637] "WSCD1" "MKRN3" "H2AC6" "MAP6D1" "OXTR" "PENK"
## [643] "MAB21L2" "GPR3" "ZNF804B" "BGN" "LHFPL1" "TCEAL7"
## [649] "TMEM119" "CCBE1" "RIPK4" "TENT5C" "RFLNB" "LHFPL6"
## [655] "FOXL2" "OLFML1" "KIRREL1" "ARSI" "LRRC55" "ST6GALNAC3"
## [661] "ADRA2C" "OLIG1" "PRKD1" "FOXO4" "SLITRK6" "B3GALT5-AS1"
## [667] "MANEAL" "FAM43A" "NOTUM" "RBM11" "PRKN" "METTL7A"
## [673] "ROR1" "NR2F2" "INKA1" "SHC4" "PMEL" "LINC00839"
## [679] "AGBL4" "BCL9L" "EDARADD" "GOLGA8R" "ZNF396" "FOXD2"
## [685] "PRR5" "CYP27C1" "MITF" "SLIT1" "FOXD3" "GJA4"
## [691] "PEAR1" "PALM3" "MAPK12" "HEPACAM2" "NUTM2B" "INSC"
## [697] "COL25A1" "FAM83G" "NKAIN2" "SPRED3" "APOD" "IL1RAPL2"
## [703] "BTBD8" "SPOCK3" "TDRD7" "SERPINA3" "KIF19" "RYR1"
## [709] "GRM7" "ZNF124" "ESRRG" "MME" "TLE1" "H2AC11"
## [715] "SERTAD1" "FAM110D" "KANK2" "SVIL" "UAP1L1" "COL13A1"
## [721] "FAM114A1" "S100A10" "IRAK4" "LPAR1" "NTRK1" "MT1F"
## [727] "ZNF480" "TGM2" "MIR29B2CHG" "RBM20" "RIPPLY2" "BMPR2"
## [733] "TCEA3" "HLA-DOA" "TAP2" "MICA" "DISP3" "TBC1D8"
## [739] "PCDHA9" "LGR4" "VIT" "EIF3CL" "LINC01597" "ONECUT3"
## [745] "NYNRIN" "DOK6" "FOXL2NB" "CRIP1" "GPC2" "GPSM3"
## [751] "KCTD11" "ITGA1" "MEF2B" "ANXA2R-AS1" "TNFRSF25" "PPP1R3G"
## [757] "CYTOR" "CKMT1A" "LINC02593" "SNHG14" "LMX1B-DT" "PRRT4"
## [763] "LINC01918" "C14orf132" "ZNF717" "D21S2088E" "LINC00858" "PRAC2"
## [769] "KHDC1-AS1" "TFAP2A-AS1" "HOXB-AS1" "DNM3OS" "FOXD3-AS1" "LINC-PINT"
## [775] "LINC00865" "AJM1" "HOTAIRM1" "TWIST2" "C12orf75" "L3MBTL2-AS1"
## [781] "ARHGEF7-AS2" "CKMT1B" "PRSS56" "WAKMAR2" "L1TD1" "AQP1"
## [787] "PNMA2" "CD302" "GLYCTK-AS1" "EFNA4" "TMEM35B" "DBNDD2"
## [793] "H2AJ" "KCTD13-DT" "APELA" "GDNF-AS1" "FMN1" "PCDHA11"
## [799] "TMEM150C" "LINC01234" "CARMN" "CACNA1G-AS1" "LINC02762" "SELENOP"
## [805] "SNHG18" "LRRC24" "MAGEL2" "B3GAT1-DT" "TRIL" "LINC01152"
## [811] "LINC01956" "FOXN3-AS1" "FRRS1L" "CDH3-AS1" "CLEC19A" "ISY1-RAB43"
## [817] "MIA" "LINC00621" "LINC00672" "GDF10" "ZNF561-AS1" "S1PR2"
## [823] "BSG-AS1" "MZF1-AS1" "SLC25A53" "CD24" "LINC02538" "MAP3K4-AS1"
## [829] "TRABD-AS1" "NATD1" "RAB7B" "PKD1L3" "NKILA" "PTENP1-AS"
## [835] "EXOC3L2"
## D50_AR
## [1] "SLC7A2" "MAP3K9" "TFAP2B" "MGST1" "GABRA3"
## [6] "SLC7A14" "POLA2" "CNTN1" "PTPRN" "DGKA"
## [11] "MPPED2" "NAV3" "SPTB" "JMJD6" "WIPI1"
## [16] "FOSL2" "ACTL6B" "MID2" "B4GALT1" "PPP1R13B"
## [21] "LHX5" "ITGA6" "RAPGEF4" "MYO15A" "HAUS4"
## [26] "TBC1D2" "SYDE2" "GCAT" "HMOX1" "SLC8A3"
## [31] "RSPO4" "PAK5" "PXMP4" "SYNDIG1" "CELF4"
## [36] "LAMA1" "GLRA2" "PCSK1N" "NALCN" "FGF14"
## [41] "NDRG4" "SMPD3" "COTL1" "NDRG1" "TUBB4A"
## [46] "LSR" "SLC1A1" "APBA1" "CPEB3" "NEURL1"
## [51] "SLC9A3R1" "ZBTB16" "JHY" "TMEM109" "MDK"
## [56] "TIMELESS" "PRDM13" "VEGFA" "LOX" "IRX4"
## [61] "PDE4D" "FGF1" "STC2" "CBLB" "SLC4A3"
## [66] "REEP6" "EFHD1" "ABCB6" "ID3" "PLPPR4"
## [71] "RCAN3" "SLC8A2" "TTR" "SGIP1" "PLAGL1"
## [76] "STBD1" "ACOT2" "PPP1R3C" "MOB3B" "GRIA2"
## [81] "ENOX1" "SLITRK3" "MYOG" "PHF24" "BHLHE41"
## [86] "OPTN" "CPNE5" "GRIA3" "MCHR1" "RNF112"
## [91] "FLNC" "SYT5" "LGALS3" "SNAP25" "ATP8A2"
## [96] "CHRM3" "MYH8" "DUSP26" "BHLHE40" "IAH1"
## [101] "P2RX4" "FAIM2" "FHOD1" "RAPGEF5" "SCN2A"
## [106] "RALGPS1" "PRCP" "GLCE" "FBN2" "RBP5"
## [111] "PHLDA1" "SDSL" "SLC46A3" "SYT16" "CELF6"
## [116] "LMTK3" "IGLON5" "FHAD1" "SEMA6C" "TMEFF2"
## [121] "ABCA12" "PHLDB2" "TMEM108" "AMT" "TNFAIP8"
## [126] "PRSS35" "SLC2A12" "GPC3" "NR6A1" "NCAM1"
## [131] "HMGA2" "DLG2" "MFSD6" "SERP2" "GRIA4"
## [136] "NRSN1" "PTPRR" "CACNA2D1" "CABYR" "SLA"
## [141] "GPR61" "KCNS2" "SYN2" "STC1" "CLIC6"
## [146] "CFAP157" "SPTBN4" "CELF5" "PLXDC1" "GRIN2C"
## [151] "CYGB" "TEDC2" "B3GALT2" "IER5" "RFTN2"
## [156] "VSNL1" "INAVA" "CADPS" "PRSS12" "NPY1R"
## [161] "EDIL3" "RNF180" "GRIK2" "STK17A" "ADCY1"
## [166] "CSMD3" "CACNB2" "SCN3B" "TMEM130" "C18orf54"
## [171] "CACNG2" "SCG5" "PBX3" "ATCAY" "HID1"
## [176] "GRM5" "ZNF354A" "TMEM266" "FAM153A" "IRX1"
## [181] "KSR2" "DLK2" "CES4A" "ARPP21" "TTC9B"
## [186] "SPSB4" "CHST1" "LINC01106" "LRRTM4" "MAMSTR"
## [191] "EPS8L2" "KCNA2" "RPRM" "PCDHB9" "ADAMTSL1"
## [196] "AMER3" "SHISA3" "TMTC2" "TMEM151A" "MROH1"
## [201] "ZNF154" "NRXN1" "MYL11" "LINC00304" "UNC5C"
## [206] "TSPEAR-AS2" "SLC8A1" "EFHC2" "KCND2" "CEND1"
## [211] "RALYL" "TCEAL2" "ROBO2" "PDIA2" "SRL"
## [216] "KCNIP4" "IKZF1" "IRS2" "FAM228A" "MIR22HG"
## [221] "FSCN2" "ESPN" "LHFPL3" "VWC2" "SKOR1"
## [226] "GREB1" "ZNF836" "AFAP1" "H2BU1" "LRRC8B"
## [231] "COL4A6" "DMBX1" "DNM3" "HMGN5" "SLC29A3"
## [236] "GRIN3A" "RYR3" "RASGEF1A" "SOWAHA" "ZNF525"
## [241] "NHSL2" "LINC02731" "PCDHA5" "LOH12CR2" "TRIM71"
## [246] "XKR4" "CAPN14" "ARHGEF28" "BASP1-AS1" "SKOR2"
## [251] "SIAH3" "GPC1-AS1" "INO80D-AS2" "NUTM2E" "DIRC3"
## [256] "STXBP5-AS1" "ANKRD65" "C2orf74" "ARHGDIG" "PCDHGC4"
## [261] "LINC00461" "HS3ST5" "TMEM158" "PCDH10-DT" "LYN"
## [266] "MIR100HG" "LINC02293" "LINC02883" "SCX" "STAM-DT"
## [271] "XKR7" "PCDHGA4" "GABRQ" "UNC5C-AS1" "ZSWIM8-AS1"
## [276] "PCDHB16" "CSGALNACT2-DT" "INSIG1-DT" "TMEM271" "LINC02334"
## [281] "SEPSECS-AS1" "PEG13" "LINC01902" "DERPC"
## D50_HT
## [1] "TNMD" "STPG1" "TMEM176A" "PDK4" "SLC25A13" "MCUB" "CROT"
## [8] "SOX8" "ITGA2B" "CACNG3" "ALDH3B1" "SCIN" "PAX6" "BAIAP3"
## [15] "E2F2" "MLXIPL" "CD9" "NCAPD2" "LRRC23" "SYT7" "ANLN"
## [22] "BRCA1" "EHD3" "TACC3" "STMN4" "PLEKHB1" "GRAMD1B" "DEPDC1"
## [29] "TYMP" "VRK2" "ARHGAP31" "DEPDC1B" "TNC" "PREX2" "ANO2"
## [36] "NEDD4L" "RAD51" "POLQ" "MSMO1" "NRIP2" "ENTPD2" "OPN3"
## [43] "HHAT" "GYG2" "F7" "RASGRF1" "YBX3" "MPC1" "EYA2"
## [50] "CNN2" "ABCA7" "HMG20B" "MCM10" "PACC1" "TLE2" "NGEF"
## [57] "ASPM" "KIF26A" "PFKP" "PHKA1" "COASY" "ACSL4" "PRR11"
## [64] "PTPN3" "CHAT" "TRIP13" "HMMR" "EVC" "NDE1" "IRAG1"
## [71] "MCM2" "GSDMB" "GLI2" "TEAD2" "CA12" "ENO1" "SEMA3A"
## [78] "GTSE1" "CACNG5" "WDR62" "ARHGAP15" "FMO4" "RGS11" "SPAG5"
## [85] "TPD52" "ACACB" "GPC4" "MBNL3" "STXBP2" "NAALAD2" "SLC25A43"
## [92] "NEBL" "RBFOX1" "SLC1A3" "LXN" "FDFT1" "OPHN1" "EPB41L2"
## [99] "EPHA6" "SLC4A4" "CHRNA3" "KCNN2" "NDC80" "TCF7" "CDH7"
## [106] "ARG2" "STK17B" "PGR" "TRAF5" "PLOD1" "KIF3C" "MECOM"
## [113] "OVGP1" "ORC1" "RAD54L" "MAST2" "EPDR1" "HBQ1" "MT3"
## [120] "AURKA" "GP6" "TPX2" "CPXM1" "TESC" "FUS" "BIRC5"
## [127] "LAG3" "YPEL3" "IRAK3" "KIF4A" "DLL3" "ABCC6" "NLRP1"
## [134] "ZFHX4" "RGS17" "SLC7A8" "SEMA6A" "CLSPN" "TGFB2" "CDC45"
## [141] "ADA2" "XYLB" "CDC6" "EPB41L4B" "SH2D3C" "CRTAC1" "PCDH11Y"
## [148] "HNRNPM" "SLC7A4" "SEZ6L" "CENPM" "SEPTIN3" "SLC5A4" "MCM5"
## [155] "TSPO" "RASD2" "APOL4" "PNPLA3" "KHNYN" "COCH" "POLE2"
## [162] "PYGL" "CCDC198" "PAPLN" "NFATC4" "VSX1" "MYBL2" "PABPC1L"
## [169] "HRH3" "TRIB3" "E2F1" "AHCY" "FAM83D" "ST8SIA5" "PRPS2"
## [176] "CHRDL1" "ZC3H12B" "KLF8" "SRPX2" "OLFM4" "CORO1A" "HAS3"
## [183] "NECAB2" "NME4" "SLC7A5" "EEF2K" "SYT17" "CORO2B" "ACSBG1"
## [190] "IGDCC4" "FAM189A1" "OIP5" "EYA1" "STK3" "PYCR3" "ARHGEF10"
## [197] "MCM4" "IL27RA" "ASF1B" "SYDE1" "AURKC" "CCNE1" "PRX"
## [204] "MYH14" "LIG1" "TMEM59L" "ZC3HAV1" "CAV2" "HOXA2" "VIPR2"
## [211] "EVX1" "CPVL" "MINDY4" "NPTX2" "TMEM176B" "GLI3" "TLE4"
## [218] "SUSD1" "AKNA" "RLN2" "KCNT1" "DDX58" "GLIS3" "PDLIM1"
## [225] "CDH23" "SPOCK2" "SH3PXD2A" "SYNGR2" "LGALS3BP" "DHX58" "PHOX2B"
## [232] "NFKB1" "NCAPG" "PPARGC1A" "CTSC" "CCDC34" "B3GAT1" "UNC93B1"
## [239] "NECTIN1" "PTPMT1" "SYT10" "LIN7A" "GLI1" "FOXM1" "PRMT8"
## [246] "RAD51AP1" "MGP" "SLC38A1" "TBC1D30" "GAPDH" "CDCA3" "NEDD9"
## [253] "MCM9" "RIPOR2" "FBXO5" "SRSF3" "MCM3" "GLP1R" "BMP5"
## [260] "E2F3" "BVES" "COL9A1" "B3GAT2" "PACRG" "PDE10A" "TTK"
## [267] "HMGCS1" "KIF20A" "TMCO6" "PCDHB6" "CCNG1" "SLC12A7" "GNPDA1"
## [274] "LIFR" "CPEB4" "HRH2" "SMC4" "BCHE" "ECT2" "GBE1"
## [281] "RTKN" "KCNIP3" "TP53I3" "GPD2" "CENPA" "SLC30A3" "LOXL3"
## [288] "ACADL" "DNAH6" "TPO" "ID2" "SLC1A4" "ATP6V1B1" "PAPPA2"
## [295] "ERRFI1" "HDAC1" "LEPR" "PLA2G4A" "RPE65" "TTF2" "BMP8B"
## [302] "ST6GALNAC5" "IGSF21" "KIF17" "RAB29" "CDC20" "TSPAN1" "F3"
## [309] "NEK2" "CENPF" "KIF14" "FILIP1" "PMFBP1" "SLC16A7" "ARMC2"
## [316] "TGIF2" "PCDH17" "ELL2" "PHF19" "IRF2BPL" "LTBP2" "PPP4R4"
## [323] "TGFB3" "ESRRB" "GPR75" "HELLS" "KCNIP2" "ARAP3" "TNN"
## [330] "CENPL" "MASTL" "SMAD9" "DUSP4" "ADRA1A" "EPHX2" "SCPEP1"
## [337] "FAM117A" "NCAPH" "ADCY7" "TSHZ3" "KCNJ8" "A1BG" "KIF18A"
## [344] "FABP3" "CPXM2" "TMEM54" "ANXA11" "PTGFR" "HOXA7" "CHST3"
## [351] "ZWINT" "CDKN2C" "CENPK" "NCKAP1L" "CDK2" "STIL" "HJURP"
## [358] "CKS2" "SLC12A4" "SDC4" "CHST8" "IQSEC2" "SERPINB6" "AHNAK"
## [365] "DOK4" "CLYBL" "ABCC4" "HROB" "BARHL1" "PAX8" "CD70"
## [372] "FAM182A" "PAX1" "GDF5" "NECAB3" "ID1" "XRCC3" "THRA"
## [379] "DLGAP5" "FGD3" "AUNIP" "KLF2" "PKMYT1" "WFIKKN1" "METTL25"
## [386] "YWHAH-AS1" "SPECC1" "MYO1B" "MYO5C" "TMOD2" "DLL4" "CLN6"
## [393] "TPH1" "DCTD" "PIMREG" "PLD2" "PUS7L" "AJUBA" "MIS18BP1"
## [400] "CDO1" "SGO1" "SAT1" "KIF1A" "ARPC1B" "PGPEP1" "HRC"
## [407] "OLFM1" "HELZ2" "CALY" "FIBCD1" "THEMIS2" "SLC35D2" "C1QL1"
## [414] "RFTN1" "AOC3" "AOC2" "IL13RA1" "TOP2A" "ZNF132" "PODNL1"
## [421] "DNAJB1" "ENOSF1" "PTPRE" "COQ3" "TRIM47" "PCBD2" "PCNA"
## [428] "ATP1A4" "NES" "TOE1" "LPIN3" "VSTM2L" "PATJ" "CCNA1"
## [435] "TRPC4" "RFC3" "AMPD3" "TEX15" "TTC9" "CCNB1" "VAV3"
## [442] "PSRC1" "TRIM45" "MYCN" "ANO3" "FST" "ECHDC3" "CDCA8"
## [449] "DSC2" "DTNA" "CEMIP2" "HRK" "TMEM243" "CD36" "HTR1B"
## [456] "EPHA7" "PRPH" "GLS2" "TROAP" "ESPL1" "HNRNPA1" "FBXL8"
## [463] "CCDC102A" "RGS8" "RNASEL" "USP44" "SLC41A2" "PCDH8" "RNASEH2B"
## [470] "CKAP2" "BORA" "MYCBPAP" "BRIP1" "GYPC" "SMC2" "KLF4"
## [477] "TMOD1" "DSCC1" "CCN3" "TCF19" "IER3" "ATAT1" "MYO7A"
## [484] "SYTL2" "RAB30" "DDX60" "ARHGAP20" "NUSAP1" "KIF23" "KNL1"
## [491] "UACA" "TMEM62" "FNBP1L" "ARHGAP29" "CENPO" "MYOF" "KIF11"
## [498] "DUSP5" "CEP55" "KIF20B" "ENTPD1" "PLCE1" "BARD1" "SLC40A1"
## [505] "PPCDC" "FAM13A" "BMPR1B" "PRDM5" "FRAS1" "SHROOM3" "CENPE"
## [512] "SLC39A8" "SHISAL1" "TMEM117" "GLIPR1" "DUSP6" "GAS2L3" "RDH16"
## [519] "BRCA2" "ESYT1" "VPS37B" "RHOF" "DIAPH3" "CBLN3" "MDGA2"
## [526] "DUOXA1" "PSTPIP1" "PIF1" "FANCI" "TICRR" "TGFB1I1" "MARVELD3"
## [533] "ADAMTS18" "CDH13" "KSR1" "TOM1L1" "ADCYAP1" "NFIC" "IFITM3"
## [540] "HUNK" "APP" "CACNG8" "EPHA2" "CNKSR1" "C1orf216" "C1orf94"
## [547] "PLK4" "MAP3K6" "KIF2C" "MOB3C" "BARHL2" "C1orf162" "NUF2"
## [554] "CASQ1" "RGS16" "LHX9" "SELENBP1" "OAZ3" "GABPB2" "DTL"
## [561] "DYRK3" "SLC27A3" "GDF7" "CHAC2" "ABHD1" "FBLN7" "AFF3"
## [568] "NXPH2" "SUMF1" "ACKR3" "FANCD2" "CTDSP1" "GRIP2" "IL17RD"
## [575] "IGSF11" "NR1I2" "BOC" "DGKQ" "SCD5" "TIFA" "CCNA2"
## [582] "USP53" "PDGFC" "PIK3R1" "LIX1" "ZNF300" "GFOD1" "TRIM7"
## [589] "TNFRSF21" "RASGEF1C" "SCUBE3" "GABRR1" "ABRACL" "MTFR2" "TIAM2"
## [596] "CREB5" "CDCA5" "TMEM168" "NCAPG2" "SH3KBP1" "MSN" "CHST7"
## [603] "LPAR4" "GINS4" "CRH" "PMP2" "ATP6V0D2" "PLIN2" "CDKN2A"
## [610] "IDNK" "SHC3" "GSN" "ST8SIA6" "RGR" "MKI67" "FUOM"
## [617] "GSTO1" "SERPING1" "RPS3" "TTC12" "GLB1L2" "GRIK4" "INCENP"
## [624] "CHEK1" "KIRREL3" "DSN1" "ALDOA" "FAM124A" "PRSS23" "DOCK1"
## [631] "PIH1D2" "KCNA6" "MAT1A" "TEX30" "ME3" "ANO4" "POU4F2"
## [638] "NR3C2" "INPP1" "CENPU" "CCDC122" "ZNF385D" "SLC35F4" "PARP8"
## [645] "MGAT5" "PSTPIP2" "SPC25" "HOMER1" "ZSCAN1" "SPARCL1" "RASGRP3"
## [652] "ZIC1" "CENPH" "SYCP2L" "BMP6" "LPCAT1" "C16orf89" "CMTM7"
## [659] "CD8A" "KCNJ16" "DDAH1" "ANKFN1" "THY1" "JPH3" "UCHL1"
## [666] "TNIK" "PGM5" "TMPRSS15" "NCAM2" "JAM2" "ADAMTS5" "SKA1"
## [673] "APCDD1" "PIEZO2" "USP43" "RAB6B" "EME1" "ACSS1" "ADCY8"
## [680] "CFAP70" "KCNMA1" "SFXN2" "FUT6" "FBXO43" "HKDC1" "MAPK13"
## [687] "ATAD2" "FRRS1" "BUB1B" "SST" "NMNAT2" "ATP2B2" "NRG1"
## [694] "STEAP2" "FZD1" "CACNA1D" "CCNB2" "ETS2" "DRC1" "MEGF11"
## [701] "SLC30A2" "UBXN11" "GALNT14" "DZIP1L" "CDC25C" "H4C8" "GDPD5"
## [708] "SLC45A3" "F11R" "CCDC24" "IGF2BP1" "CBR1" "HK2" "CELF3"
## [715] "THEM4" "TCHH" "NPR2" "ZNF233" "TNFRSF13C" "ABCG1" "PDE9A"
## [722] "C21orf58" "ZNF761" "PKN3" "RUSC1" "NBEAL2" "RECQL4" "LRRC56"
## [729] "ITGA5" "ZNF385A" "PLCD3" "SPC24" "CCNF" "LBHD1" "PDPN"
## [736] "CAMK2N1" "WNT4" "SNX7" "NTNG1" "AKNAD1" "ATXN7L2" "CADM3"
## [743] "KCNJ9" "PEA15" "OLFML2B" "ACP6" "KCNF1" "KCNJ3" "ARHGAP25"
## [750] "FZD5" "SLC15A2" "LMOD1" "ADORA1" "CIP2A" "SGO2" "SERPINI1"
## [757] "NUAK2" "RPL22L1" "PTPN13" "C4orf36" "PPM1K" "KIF15" "FYCO1"
## [764] "KLF15" "ABLIM2" "CDC25A" "POC1A" "ETNPPL" "MAD2L1" "SMIM43"
## [771] "NPY5R" "HHIP" "ZNF474" "FABP7" "TLX3" "HCN1" "NEUROD6"
## [778] "PTTG1" "CDCA7L" "SP8" "HEY1" "FABP5" "HNF4G" "EN2"
## [785] "NFIL3" "FXN" "PCDH19" "WNK2" "MELK" "HECTD2" "SKA3"
## [792] "DDIAS" "LRR1" "ZNF22-AS1" "TMEM63C" "NGB" "AKR1E2" "DRGX"
## [799] "HTRA1" "PLEKHF1" "NUDT13" "LMO1" "CENPN" "WEE1" "PRKCB"
## [806] "CPLX4" "CFAP52" "TVP23A" "SLFN5" "PCLAF" "LDHD" "RBPMS2"
## [813] "PLK1" "NEMP1" "STX3" "MTMR10" "MS4A8" "MAPRE2" "NAT16"
## [820] "SGSM1" "ACSF2" "ART5" "MVD" "CDT1" "AXL" "PPP1R14A"
## [827] "CHAF1A" "TRPV3" "TK1" "ATG16L2" "CCDC88B" "PBK" "PNOC"
## [834] "GLYCTK" "IRF2BP2" "SCN11A" "MFSD2A" "TNXB" "LGI3" "PHYHIP"
## [841] "GSTM4" "SHOX2" "ENHO" "LGALS9" "RGS14" "CKAP2L" "HIC2"
## [848] "BUB1" "AGPAT2" "LDB2" "P2RY1" "WNT10B" "FRMPD4" "TMEM42"
## [855] "GPR37L1" "CMTM8" "CDK1" "FOS" "SLC30A1" "MGMT" "TRABD"
## [862] "ZNF296" "CDCA4" "MTSS1" "JUNB" "SHCBP1" "ESCO2" "LURAP1"
## [869] "COL24A1" "NEUROD2" "CXXC5" "BCL2" "RRM2" "SRGAP2C" "MAL"
## [876] "MBOAT1" "CEBPB" "CSDC2" "RCAN2" "PRSS27" "RSPH9" "FUT9"
## [883] "SMPDL3A" "EFEMP2" "THEMIS" "CYP7B1" "METAP1D" "LVRN" "SH3RF3"
## [890] "HSPA6" "ADAMTS20" "GLRX" "SYT12" "PPP1R3B" "TRIB1" "CEP83"
## [897] "SCAI" "SUSD5" "PLK3" "MARCHF3" "TCAP" "TLR1" "NWD2"
## [904] "EVX2" "EXO1" "CRMA" "ZCCHC12" "TMEM81" "KY" "FGFBP3"
## [911] "AMZ1" "ZIC4" "UBE2C" "TRAF6" "FAM182B" "CSRP2" "VWA3A"
## [918] "CCNE2" "MCTP1" "TSGA10IP" "SUGCT" "RMI2" "PRIMA1" "ETV4"
## [925] "HOXD8" "SPHK1" "ACBD7" "DMRTA1" "DNAJC30" "CLK2" "LPCAT4"
## [932] "KBTBD11" "ZNF843" "IRX5" "TYMS" "PXMP2" "TYMSOS" "SIX5"
## [939] "ACER2" "CLVS1" "HASPIN" "FAM20C" "ODF3B" "DPY19L2" "PDE4DIP"
## [946] "ZNF114" "SH2D4B" "GEN1" "AQP11" "NEUROG2" "MAF" "ZNF713"
## [953] "RPP25" "CPNE7" "EFCAB13" "APOLD1" "PFAS" "HES7" "VWA1"
## [960] "FJX1" "ZBTB42" "RPRML" "ANKRD18A" "LYNX1" "TH" "RCC1"
## [967] "PLD5" "ALX1" "GAS1" "GSX2" "SSTR2" "ZNF594" "MAB21L1"
## [974] "GPR157" "FANCB" "C6orf223" "TIGIT" "RTKN2" "TRIM49B" "FAM181B"
## [981] "CREB3L2" "KCNA4" "NXPH4" "KPNA2" "NTM" "KCNB2" "IGIP"
## [988] "RGS6" "PAPPA" "GRID1" "GALNT9" "ADGRG3" "CADM1" "SLC25A21"
## [995] "SLC25A10" "BEGAIN" "FAM43B" "CSMD1" "C2CD4C" "POTEC"
## [ reached getOption("max.print") -- omitted 357 entries ]D25_AR:D50_AR
all_intersections$`D25_AR:D50_AR`
## [1] "FZD10" "TFCP2" "SLC15A4" "TPPP3" "PFKFB3" "H2AW" "BCAM"
## [8] "ZNF605" "ZNF100" "PCDHA4" "PCDHA13" "FZD10-AS1" "LHX1" "LHX1-DT"D25_AR:D50_HT
all_intersections$`D25_AR:D50_HT`
## [1] "DSG2" "GPR50" "CLU" "LMO2" "GRIA1" "PPP1R32" "SERINC5" "CRABP1"D25_HT:D25_AR
all_intersections$`D25_HT:D25_AR`
## [1] "BMP7" "BMF" "DNAI1" "SSUH2" "MNS1"
## [6] "LEF1" "HDC" "MYBPC1" "BLOC1S5-TXNDC5" "TXNIP"D25_HT:D50_AR
all_intersections$`D25_HT:D50_AR`
## [1] "RUNX1T1" "SORBS1" "EEF1A2" "PCYT1B" "SEMA5A" "CDH9"
## [7] "RBP1" "FNDC4" "BCL11A" "NXPH1" "MMP24" "NOTCH2"
## [13] "STK26" "TNS3" "ARHGAP24" "AMIGO2" "COL2A1" "DISP2"
## [19] "CCDC33" "KIFC3" "GAS8" "CRABP2" "HMGCLL1" "GRM1"
## [25] "ANKRD29" "ROBO3" "ADAMTS1" "VCAM1" "UNCX" "EFNA1"
## [31] "DSCAM" "NEGR1" "SLITRK1" "BACE2" "OAF" "HS6ST3"
## [37] "CPNE4" "LRRTM3" "C2orf72" "ARHGEF35-AS1"D25_HT:D50_HT
all_intersections$`D25_HT:D50_HT`
## [1] "HS3ST1" "KLHL13" "SKAP2" "GCFC2" "CRLF1" "TMEM132A"
## [7] "DNAH9" "GAS7" "TKTL1" "CAMK1G" "NFIX" "TENM1"
## [13] "MTMR11" "ATP1A2" "ZNF582" "CD74" "ADGRA2" "FAS"
## [19] "TMSB10" "COL9A2" "FOXC1" "PARP12" "PRDM6" "NGFR"
## [25] "ME1" "TGFBR3" "FGF10" "NCK2" "SPEG" "ST6GAL1"
## [31] "ZNF37A" "PAX2" "MCAM" "ADCY2" "SESN1" "LYRM2"
## [37] "EFR3B" "PPEF1" "BAX" "ADAMTS2" "GNAO1" "SLC4A11"
## [43] "LAMB1" "WDR76" "COL9A3" "COMT" "CYP26A1" "MFNG"
## [49] "LGALS1" "SOX10" "TIMP3" "RIN3" "DHRS2" "SLCO4A1"
## [55] "RNF125" "TIMP1" "SYTL4" "FGF9" "DGKH" "MAPK3"
## [61] "GDPD3" "TRPA1" "SLC1A6" "TFPI2" "LHX2" "ENG"
## [67] "SH3GL2" "RASSF4" "TLX1" "SFXN3" "PNPO" "SOX6"
## [73] "TNS2" "ELK3" "OAS3" "MDGA1" "KHDRBS2" "ASCC3"
## [79] "PCDHB5" "CDH6" "PDGFRB" "UNC5A" "EHHADH" "MRPL3"
## [85] "POMC" "ITGA4" "HPCAL1" "QPCT" "DLX2" "PRRX1"
## [91] "KIF21B" "ZNHIT6" "SLC2A1" "NENF" "PROX1" "NRP2"
## [97] "RAB32" "ONECUT2" "PYROXD2" "ACAT2" "KIAA1217" "EGR1"
## [103] "TNFRSF10B" "CAT" "ARL4A" "GLIPR2" "PLP1" "CDKN1A"
## [109] "MT2A" "TNFSF9" "CITED1" "FLRT1" "PLEKHG3" "TMEM35A"
## [115] "LRRC61" "GNG11" "RASL11B" "LIF" "DOCK4" "FEZF1"
## [121] "ISLR" "LOXL1" "E2F8" "SOX15" "CD68" "MTUS1"
## [127] "RPS4Y1" "GAMT" "GDPD2" "SH3BP4" "COL5A1" "MED18"
## [133] "HIP1R" "PNCK" "DUSP9" "EDA2R" "RAB11FIP4" "SLC6A6"
## [139] "GFPT2" "SLC6A11" "NUP210" "RAP1GAP2" "BCAN" "PPP1R3D"
## [145] "DCLK1" "POSTN" "STARD13" "NTS" "SWAP70" "RNF122"
## [151] "CAMK1" "SYT6" "CMPK2" "DAGLA" "ADAM19" "BICDL1"
## [157] "MDM2" "SP110" "SERPINE2" "DRAM1" "GPNMB" "GAD2"
## [163] "CTSV" "MYC" "TFAP2A" "FOXF2" "SLCO5A1" "ITGA11"
## [169] "ZNF280D" "IFI44L" "IFI44" "SIX3" "ZNF365" "STAT4"
## [175] "HECW2" "PARP9" "SEMA7A" "HERC5" "CPNE8" "FOXN4"
## [181] "GRTP1" "ARMH4" "NEIL1" "ST8SIA2" "TIGD7" "MAPK4"
## [187] "STAC2" "PLPP2" "PGGHG" "HMCN1" "CGN" "EFNA3"
## [193] "CNGA3" "SLC4A10" "DLX1" "SPAG16" "ITGA9" "IGFBP3"
## [199] "DIAPH2" "RGS20" "STOM" "LCN9" "PROSER2" "PAOX"
## [205] "RGS10" "CDH8" "GPM6A" "FREM2" "TMEM86A" "ABTB3"
## [211] "GFRA1" "TRIM36" "PLEKHH2" "ZNF117" "RASSF3" "NMRAL1"
## [217] "LGI4" "UBASH3B" "PITPNC1" "OBSCN" "DKK2" "PTPRN2"
## [223] "AFF2" "WIF1" "MPV17L" "MMP14" "C2CD2" "PSMG3"
## [229] "XKR8" "CLSTN2" "SLC13A3" "DMTN" "S100B" "LY6E"
## [235] "FDXR" "ZNF75A" "AK4" "NFIA" "DDR2" "SPATA18"
## [241] "TAFA4" "CDS1" "PTX3" "APBB2" "DTX3L" "PRKCD"
## [247] "ARHGEF3" "EXO5" "ERMAP" "ITGA2" "F2RL2" "CMBL"
## [253] "EGFLAM" "UBLCP1" "ACSL6" "DLC1" "SPIDR" "VEGFD"
## [259] "PHOX2A" "PKNOX2" "E2F7" "PACSIN3" "KCNC2" "ADAMTS15"
## [265] "IKBIP" "ALKBH3" "TMEM100" "CHRFAM7A" "ELFN2" "GREM1"
## [271] "TUBA1C" "ZNF528" "PLIN4" "RAB3IL1" "SCARA3" "MMADHC"
## [277] "COL3A1" "GFRA2" "INPP5D" "CHST14" "PCSK9" "KCNK9"
## [283] "ONECUT1" "GPRC5C" "EMB" "SIX2" "DLGAP1" "POLH"
## [289] "PRKCE" "NPTX1" "CLCN5" "DSEL" "ZNF562" "ECEL1"
## [295] "GATM" "CFAP46" "PRNP" "FRMD5" "FRMD3" "ZMAT3"
## [301] "ZNF596" "RARG" "MYD88" "ZNF680" "PARP14" "PTPRM"
## [307] "VEGFB" "TNFRSF10C" "JUP" "HAP1" "CTSF" "MSRB3"
## [313] "PHLDA3" "ZNF25" "ALG10B" "FOSL1" "MTLN" "TUBB6"
## [319] "ZNF135" "HSD11B2" "RIMS2" "RNF152" "BDNF" "BOK"
## [325] "TCERG1L" "TCIM" "KCNA3" "ANXA2R" "ANXA2R-OT1" "ZNF619"
## [331] "ZNF454" "POGLUT3" "NRIP1" "TSPYL5" "ZFP3" "ARSJ"
## [337] "FAM83H" "AEN" "TMEM132E" "TMIE" "ZNF875" "CHST15"
## [343] "KCNIP1" "PLCB1" "RNF32-DT" "SPNS2" "CHST6" "MAGEA2B"
## [349] "CCDC125" "BCOR" "FHL3" "TRIM61" "ZNF703" "ANKRD45"
## [355] "CFAP91" "PNMA3" "ZNF730" "TBX1" "CNTN2" "ALDH1A3"
## [361] "CSF1" "TXNRD2" "LRRC26" "SRY" "TMEM121" "RPS27L"
## [367] "INPP5J" "AHNAK2" "OLFML2A" "NDUFA4L2" "PRAME" "C11orf87"
## [373] "IFIT1" "RTN4RL1" "SHOX" "ZNF225-AS1" "ANKRD37" "ZNF501"
## [379] "HPDL" "PDZD7" "WDR86" "SAMD11" "POTEE" "PRELP"
## [385] "SHISA6" "H1-0" "SP6" "PLAC9" "ZNF527" "ZNF33A"
## [391] "PAX8-AS1" "FAM217B" "ZNF107" "NTNG2" "ARL9" "CACNA1H"
## [397] "AJAP1" "POTEF" "ZNF502" "POTEI" "ARID5A" "ZNF585A"
## [403] "ZNF138" "ZNF429" "ZNF470" "ADARB1" "PDGFA" "EME2"
## [409] "H2BC12" "HES5" "ZNF71" "ZNF560" "ZNF273" "ZNF248"
## [415] "HOXC4" "ZNF583" "ZNF534" "EIF1AY" "INPP5F" "CCDC152"
## [421] "CSAG1" "TCEAL5" "HSPA1A" "HLA-C" "INSYN2B" "PNMA8B"
## [427] "LRRC10B" "MUC19" "C21orf62" "GOLGA8O" "HLA-A" "GPX3"
## [433] "MAGEA12" "ERV3-1" "EMP2" "LTB4R" "FAM66B" "SCRT2"
## [439] "HMX1" "LINC01139" "LINC03010" "CEBPZOS" "LINGO3" "LINC02076"
## [445] "EBF2" "PLXNA4" "ZNF880" "POTEM" "ADM5" "MIR3659HG"
## [451] "LINC01980" "RUSC1-AS1" "LINC01748" "SOX21-AS1" "MIR34AHG" "ZBTB46-AS2"
## [457] "PSMG3-AS1" "TSPAN19" "GOLGA8N" "LNCTAM34A" "HLA-B" "DANT2"
## [463] "GNAS-AS1" "FAM88E" "FOXD2-AS1" "SHISA9" "LINC00649" "PCDHGC3"
## [469] "NECTIN3-AS1" "PDE6B-AS1" "SOX2-OT" "ZNF512" "PTCHD4" "NEAT1"
## [475] "LINC00682" "SLCO5A1-AS1" "MIR4458HG" "CASC9" "LINC02972" "PVT1"
## [481] "GOLGA8K" "AGA-DT" "CHCHD10" "YPEL3-DT" "LINC00491" "LINC02600"
## [487] "LINC02315" "FOXD1" "ZFHX4-AS1" "PCDHGA10" "PCDHGB4" "AP5B1"
## [493] "SALL3" "LINC02306" "DIO3OS" "LINC02301" "LINC02820" "TMEM179"
## [499] "ZNF710-AS1" "PWRN1" "SPON1" "LINC01896" "PARD6G-AS1" "KC6"
## [505] "ZNF285" "MAGEA2" "CSAG3" "MIA-RAB4B" "ZNF470-DT" "LINC01297"
## [511] "TUBGCP5"D50_HT:D50_AR
all_intersections$`D50_HT:D50_AR`
## [1] "PRKAR2B" "ITGA3" "TAC1" "SYT13" "CPS1" "TNFRSF1B" "FLT4"
## [8] "CAMK2B" "SEZ6" "FGFR2" "PRKCZ" "ATP2B3" "REEP1" "RORA"
## [15] "LNX1" "PPP2R2C" "TRIP6" "PUS7" "MYH7" "FKBP5" "CACNA1I"
## [22] "GINS1" "SALL4" "SLC32A1" "MAP1LC3A" "NOL4" "HSF4" "CBLN1"
## [29] "ICAM5" "PLA2G4C" "PLEKHA4" "ADAP1" "CHN2" "TFR2" "RARRES2"
## [36] "EBF3" "NEIL3" "CRYAB" "GMNN" "ARFGEF3" "HBEGF" "GABRG2"
## [43] "HES1" "SLC5A7" "DNAJC6" "PADI2" "CA14" "ATP10B" "IQSEC3"
## [50] "MND1" "SV2C" "GRM4" "PACSIN1" "MIR9-1HG" "OPRL1" "BCL2L12"
## [57] "HIVEP3" "TUBA4A" "CDKN2D" "EGLN3" "CBFA2T3" "GINS2" "LIN28A"
## [64] "TRIM22" "GPR12" "MYBPH" "ALDH1L2" "GABBR2" "ARHGEF39" "PAK6"
## [71] "STRA6" "CYP2C8" "PCDH10" "RASGEF1B" "MTTP" "RTN1" "FBLN5"
## [78] "NOL3" "RHBDL3" "TAF4B" "SLC16A3" "CBLN2" "SUSD4" "ST6GAL2"
## [85] "SCN1A" "CDCA7" "MARCHF4" "VWA5B2" "OCIAD2" "MARCHF1" "SFRP2"
## [92] "PSD2" "EML3" "CNTN5" "LYPD1" "VEGFC" "ADAMTS12" "CCDC3"
## [99] "AKR1C2" "STK32B" "JAKMIP1" "PID1" "CDH12" "GPR26" "CNTNAP5"
## [106] "GOLGA7B" "PPP2R2B" "SLC6A1" "LDLRAP1" "NPM2" "CPAMD8" "GPATCH4"
## [113] "ALPL" "GPX8" "GPR85" "MYORG" "DIRAS2" "LRFN5" "AMER2"
## [120] "RET" "BTNL9" "CDYL2" "PRTG" "YPEL4" "LDLRAD4" "NSG1"
## [127] "FSTL5" "B3GALNT1" "KCNAB1" "PROKR1" "PCDH7" "KCNK3" "KCND3"
## [134] "CDK5R2" "CALB2" "CKS1B" "ABLIM3" "IGDCC3" "DPP10" "CREG2"
## [141] "CDK5R1" "LY6H" "FIBIN" "DSCAML1" "NHLH2" "AURKB" "FAM216B"
## [148] "ARHGAP45" "HHIPL1" "CALN1" "CHEK2" "KCNQ3" "PCDH9" "POU6F1"
## [155] "MAP7D2" "ANKS1B" "GPRIN3" "PARPBP" "SYN3" "DLEU7" "MYT1L"
## [162] "MAPT" "LUZP2" "LIN28B" "DIPK1C" "DNER" "JAKMIP3" "INSYN2A"
## [169] "RASSF10" "PTPRT" "SEMA4A" "SLC6A9" "SLC6A17" "ADGRA1" "DIO3"
## [176] "NUP62CL" "CACNA1E" "HYLS1" "TUSC1" "SMOC1" "PLXNB3" "GRM3"
## [183] "INF2" "LINC02487" "COL15A1" "PCDHA7" "MIR219A2HG" "C2orf74-DT" "SYT3"
## [190] "LCNL1" "SP9" "INHBA-AS1" "LINC02470" "RFPL1S" "LINC01503" "LINC01322"
## [197] "PCP4L1" "EPHA5-AS1" "PCDHGB7" "TMPO-AS1" "LINC01619" "FIGNL2" "GRIN2B"
## [204] "EPOP"D25_AR:D50_HT:D50_AR
all_intersections$`D25_AR:D50_HT:D50_AR`
## [1] "ZNF506" "ZNF671" "UNC5B" "LRRC4C" "GLT1D1" "ZNF585B" "ZNF790-AS1"D25_HT:D25_AR:D50_AR
all_intersections$`D25_HT:D25_AR:D50_AR`
## NULLD25_HT:D25_AR:D50_HT
all_intersections$`D25_HT:D25_AR:D50_HT`
## [1] "CACNA1G" "RSPO3" "VAX1" "ANGPT1" "ZNF558" "LRRN3" "SOX11"
## [8] "PCDH18" "SILC1" "PURPL" "LINC02381" "BLACAT1"D25_HT:D50_HT:D50_AR
all_intersections$`D25_HT:D50_HT:D50_AR`
## [1] "HECW1" "CYP26B1" "SYN1" "ST3GAL1" "MAMLD1" "LRRC7" "RIMBP2"
## [8] "GUCY1B1" "ANKRD44" "TRNT1" "PCDHA6" "SERTAD4" "SLCO1A2" "MLC1"
## [15] "OLFM2" "ACTA2" "PTPN5" "LAMA4" "CHD5" "NEK6" "MSX2"
## [22] "DNAJC15" "CSMD2" "MYRF" "BCL11B" "FOXP2" "NFATC1" "SH3BP5"
## [29] "CTIF" "PI15" "MMRN1" "NTRK3" "CDH11" "CACNA1A" "RBMS3"
## [36] "NKD2" "LHFPL2" "NFIB" "FAM13C" "ADM" "CACNA1C" "DAB2"
## [43] "CA10" "UNC5D" "KIT" "CACNA2D3" "NRG2" "CILP2" "LMX1A"
## [50] "KIF26B" "INHBB" "GUCY1A1" "ZCCHC24" "DACT1" "CYYR1" "RBFOX3"
## [57] "FAM110B" "PLEKHA2" "NSG2" "TNFRSF10D" "UCP2" "GRIN1" "RNF182"
## [64] "COL18A1" "KCNH8" "SEPTIN5" "FAM183A" "C3orf70" "LITAF" "MYT1"
## [71] "TMEM229B" "MMP17" "GP1BB" "NPTXR" "CYP4F26P" "FEZF1-AS1" "ANKRD18B"
## [78] "LINC01122" "MIR210HG" "PCDHA10" "LINC02506" "ZNF528-AS1" "ARHGAP23" "COPG2IT1"D25_HT:D25_AR:D50_HT:D50_AR
all_intersections$`D25_HT:D25_AR:D50_HT:D50_AR`
## [1] "SPINK5" "TRIM4" "TMEM132D" "IFTAP" "ZNF667-AS1" "ZNF439" "ZNF829"
## [8] "ZNF471" "ZNF493" "ZFP28" "ZNF667" "PCDHA2" "MEG3" "MEG9"
## [15] "MEG8" "LINC01515" "PCDHA3" "LINC02893" "ZNF229"Gene Ontology on genes shared by Day25 HT and Day50 AR
D25_HT_D50_AR_overlapGenes <- all_intersections$`D25_HT:D50_AR` #Genes in overlap
Universe <- union(rownames(DEAList_day25_HT$HT$res), rownames(DEAList_day50_AR$AR$res)) #Union of detected genes for universe
GeneVectors <- list()
GeneVectors$DEGenes <- ifelse(Universe %in% D25_HT_D50_AR_overlapGenes, 1, 0)
names(GeneVectors$DEGenes) <- Universe
BPann <- topGO::annFUN.org(whichOnto="BP", feasibleGenes=names(GeneVectors$DEGenes),
mapping="org.Hs.eg.db", ID="symbol") %>% inverseList()
ResBP_D25_HT_D50_AR_overlapGenes <- topGOResults(Genes=GeneVectors$DEGenes, gene2GO=BPann, ontology='BP', geneSelectionFun = function(x) (x == 1),
desc=NULL, nodeSize=3, algorithm='weight01', statistic='fisher',
EnTh=1, PvalTh=0.05, minTerms=12, geneTh=3,
saveRes=FALSE)## Gene vector contains levels:##
## Building most specific GOs .....## ( 11898 GO terms found. )##
## Build GO DAG topology ..........## ( 15542 GO terms and 35379 relations. )##
## Annotating nodes ...............## ( 14387 genes annotated to the GO terms. )##
## -- Weight01 Algorithm --
##
## the algorithm is scoring 1335 nontrivial nodes
## parameters:
## test statistic: fisher##
## Level 17: 2 nodes to be scored (0 eliminated genes)##
## Level 16: 7 nodes to be scored (0 eliminated genes)##
## Level 15: 10 nodes to be scored (31 eliminated genes)##
## Level 14: 11 nodes to be scored (101 eliminated genes)##
## Level 13: 21 nodes to be scored (230 eliminated genes)##
## Level 12: 38 nodes to be scored (452 eliminated genes)##
## Level 11: 58 nodes to be scored (1630 eliminated genes)##
## Level 10: 99 nodes to be scored (3681 eliminated genes)##
## Level 9: 135 nodes to be scored (4772 eliminated genes)##
## Level 8: 171 nodes to be scored (5819 eliminated genes)##
## Level 7: 207 nodes to be scored (7440 eliminated genes)##
## Level 6: 217 nodes to be scored (9962 eliminated genes)##
## Level 5: 181 nodes to be scored (11772 eliminated genes)##
## Level 4: 105 nodes to be scored (13190 eliminated genes)##
## Level 3: 55 nodes to be scored (13917 eliminated genes)##
## Level 2: 17 nodes to be scored (14137 eliminated genes)##
## Level 1: 1 nodes to be scored (14190 eliminated genes)custom_theme <- theme(
panel.background = element_blank(), # No background color
panel.border = element_rect(color = "black", fill = NA, size = 0.5), # Black border around panels
panel.grid.major = element_line(color = "grey90", size = 0.5), # Grey major grid lines
panel.grid.minor = element_blank(), # No minor grid lines
axis.text = element_text(color = "black"), # Black text for axis labels
axis.title = element_text(color = "black"), # Black text for axis titles
plot.title = element_text(color = "black", hjust = 0.5), # Black plot title, centered
legend.position = "top", # No legend
strip.background = element_blank(), # No background for facet labels
strip.text = element_text(color = "black", face = "bold") # Black, bold text for facet labels
)## Warning: The `size` argument of `element_rect()` is deprecated as of ggplot2 3.4.0.
## ℹ Please use the `linewidth` argument instead.
## This warning is displayed once every 8 hours.
## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was generated.## Warning: The `size` argument of `element_line()` is deprecated as of ggplot2 3.4.0.
## ℹ Please use the `linewidth` argument instead.
## This warning is displayed once every 8 hours.
## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was generated.ResOrdered <- ResBP_D25_HT_D50_AR_overlapGenes$ResSel
ResOrdered <- ResOrdered[order(ResOrdered$Statistics, decreasing = TRUE), ]
MaxVal <- round(max(-log10(as.numeric(ResOrdered$Statistics)), na.rm=TRUE), 0) +1
ResOrdered$fillcolor <- '#ed72a9'# '#31688EFF'
ResOrdered$Term <- factor(ResOrdered$Term, levels = ResOrdered$Term)
ResOrdered <- ResOrdered %>% filter(ResOrdered$Statistics < 0.05)
ggplot(data=ResOrdered, aes(x=Term, y=-log10(as.numeric(Statistics)), size=ER)) +
geom_hline(yintercept=-log10(0.05), col='gray80', lty='longdash') +
geom_point(stat='identity', colour="black", pch=21, fill=ResOrdered$fillcolor) +
#geom_text(aes(y=0), label=ResOrdered$Term, hjust=0, size=4, color='black') +
scale_y_continuous(breaks=seq(0,MaxVal,2), labels=abs(seq(0, MaxVal, 2)), limits=c(0,MaxVal), expand=c(0.025, 0.025)) +
ylab('-log10 PValue') + xlab('') +
theme_bw() +
labs(size='Enrichment Ratio') +
theme(legend.position='right', axis.text = element_text(colour = 'black', size=12),
plot.title= element_text(face='', size=10, hjust = 0.5)) +
custom_theme +
scale_x_discrete(position = "top") +
coord_flip()
ggsave(paste0(params$OutputFolder, 'Output/Figures/', 'GO_BP_sharedGenes_D25HTandD50AR.pdf'), device = 'pdf', width = 8, height = 4)Gene Ontology on genes in Day25 HT and Day50 Overlap with SFARI genes
D25_HT_D50_AR_overlapGenesSFARI <- rownames(CompareResFlip$Significant)
GeneVectors$DEGenesSFARI <- ifelse(Universe %in% D25_HT_D50_AR_overlapGenesSFARI, 1, 0)
names(GeneVectors$DEGenesSFARI) <- Universe
ResBP_D25_HT_D50_AR_overlapGenesSFARI <- topGOResults(Genes=GeneVectors$DEGenesSFARI, gene2GO=BPann, ontology='BP', geneSelectionFun = function(x) (x == 1),
desc=NULL, nodeSize=1, algorithm='weight01', statistic='fisher',
EnTh=1, PvalTh=0.05, minTerms=12, geneTh=1,
saveRes=FALSE)## Gene vector contains levels:##
## Building most specific GOs .....## ( 11898 GO terms found. )##
## Build GO DAG topology ..........## ( 15542 GO terms and 35379 relations. )##
## Annotating nodes ...............## ( 14387 genes annotated to the GO terms. )##
## -- Weight01 Algorithm --
##
## the algorithm is scoring 0 nontrivial nodes
## parameters:
## test statistic: fisher## Warning in getSigGroups(object, test.stat): No enrichment can pe performed - there are no feasible
## GO terms!## No GO category enrichedsessionInfo()
## R version 4.1.1 (2021-08-10)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 20.04.3 LTS
##
## Matrix products: default
## BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8
## [4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
## [7] LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C
## [10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
##
## attached base packages:
## [1] grid stats4 stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] gplots_3.1.3 ggvenn_0.1.10 scales_1.3.0
## [4] DESeq2_1.34.0 colorRamp2_0.1.0 ComplexHeatmap_2.10.0
## [7] UpSetR_1.4.0 GeneOverlap_1.30.0 data.table_1.14.2
## [10] cowplot_1.1.1 RColorBrewer_1.1-3 gridExtra_2.3
## [13] sechm_1.2.0 topGO_2.46.0 SparseM_1.81
## [16] GO.db_3.14.0 graph_1.72.0 org.Hs.eg.db_3.14.0
## [19] SummarizedExperiment_1.24.0 GenomicRanges_1.46.1 GenomeInfoDb_1.30.1
## [22] MatrixGenerics_1.6.0 matrixStats_0.62.0 RNASeqBulkExploratory_0.2.1
## [25] overlapper_0.99.1 tidyr_1.2.0 dplyr_1.0.9
## [28] forcats_0.5.2 viridis_0.6.2 viridisLite_0.4.1
## [31] enrichplot_1.14.2 ggplot2_3.5.1 AnnotationDbi_1.56.2
## [34] IRanges_2.28.0 S4Vectors_0.32.4 Biobase_2.54.0
## [37] BiocGenerics_0.40.0 clusterProfiler_4.2.2
##
## loaded via a namespace (and not attached):
## [1] shinydashboard_0.7.2 utf8_1.2.2 tidyselect_1.2.0
## [4] RSQLite_2.2.12 htmlwidgets_1.5.4 TSP_1.2-1
## [7] BiocParallel_1.28.3 Rtsne_0.16 scatterpie_0.1.7
## [10] munsell_0.5.0 codetools_0.2-18 DT_0.25
## [13] withr_2.5.0 colorspace_2.0-3 GOSemSim_2.20.0
## [16] filelock_1.0.2 highr_0.9 knitr_1.40
## [19] rstudioapi_0.14 DOSE_3.20.1 labeling_0.4.2
## [22] GenomeInfoDbData_1.2.7 polyclip_1.10-0 bit64_4.0.5
## [25] farver_2.1.1 downloader_0.4 vctrs_0.6.5
## [28] treeio_1.18.1 generics_0.1.3 lambda.r_1.2.4
## [31] xfun_0.31 BiocFileCache_2.2.1 R6_2.5.1
## [34] doParallel_1.0.17 clue_0.3-61 graphlayouts_0.8.2
## [37] seriation_1.3.6 locfit_1.5-9.6 bitops_1.0-7
## [40] cachem_1.0.6 fgsea_1.20.0 gridGraphics_0.5-1
## [43] DelayedArray_0.20.0 assertthat_0.2.1 shinycssloaders_1.0.0
## [46] promises_1.2.0.1 BiocIO_1.4.0 ggraph_2.0.5
## [49] gtable_0.3.1 tidygraph_1.2.1 rlang_1.1.4
## [52] genefilter_1.76.0 GlobalOptions_0.1.2 splines_4.1.1
## [55] rtracklayer_1.54.0 lazyeval_0.2.2 yaml_2.3.5
## [58] reshape2_1.4.4 GenomicFeatures_1.46.5 crosstalk_1.2.0
## [61] httpuv_1.6.6 qvalue_2.26.0 tools_4.1.1
## [64] ggplotify_0.1.0 ellipsis_0.3.2 jquerylib_0.1.4
## [67] Rcpp_1.0.9 plyr_1.8.7 progress_1.2.2
## [70] zlibbioc_1.40.0 purrr_0.3.5 RCurl_1.98-1.7
## [73] prettyunits_1.1.1 GetoptLong_1.0.5 ggrepel_0.9.1
## [76] cluster_2.1.2 tinytex_0.42 magrittr_2.0.3
## [79] futile.options_1.0.1 DO.db_2.9 circlize_0.4.15
## [82] randomcoloR_1.1.0.1 mime_0.12 hms_1.1.2
## [85] patchwork_1.3.0 evaluate_0.17 xtable_1.8-4
## [88] XML_3.99-0.10 VennDiagram_1.7.3 shape_1.4.6
## [91] compiler_4.1.1 biomaRt_2.50.3 tibble_3.1.7
## [94] KernSmooth_2.23-20 V8_4.2.0 crayon_1.4.1
## [97] shadowtext_0.1.2 htmltools_0.5.2 later_1.3.0
## [100] ggfun_0.0.7 geneplotter_1.72.0 aplot_0.1.8
## [103] DBI_1.1.3 formatR_1.12 tweenr_2.0.2
## [106] dbplyr_2.2.0 MASS_7.3-54 rappdirs_0.3.3
## [109] Matrix_1.3-4 cli_3.6.3 parallel_4.1.1
## [112] igraph_1.3.5 pkgconfig_2.0.3 registry_0.5-1
## [115] GenomicAlignments_1.30.0 plotly_4.10.4 xml2_1.3.3
## [118] foreach_1.5.2 ggtree_3.2.1 annotate_1.72.0
## [121] bslib_0.4.0 XVector_0.34.0 yulab.utils_0.0.5
## [124] stringr_1.4.1 digest_0.6.28 Biostrings_2.62.0
## [127] rmarkdown_2.17 fastmatch_1.1-3 tidytree_0.3.9
## [130] restfulr_0.0.15 curl_4.3.3 gtools_3.9.4
## [133] shiny_1.7.2 Rsamtools_2.10.0 rjson_0.2.21
## [136] lifecycle_1.0.3 nlme_3.1-152 jsonlite_1.7.2
## [139] futile.logger_1.4.3 fansi_0.5.0 pillar_1.8.1
## [142] ggsci_3.0.0 lattice_0.20-45 KEGGREST_1.34.0
## [145] fastmap_1.1.0 httr_1.4.4 survival_3.2-13
## [148] glue_1.6.2 png_0.1-7 iterators_1.0.14
## [151] bit_4.0.4 ggforce_0.4.1 stringi_1.7.8
## [154] sass_0.4.2 blob_1.2.3 caTools_1.18.2
## [157] memoise_2.0.1 ape_5.6-2